4V3P | pdb_00004v3p

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

PDB DOI: https://doi.org/10.2210/pdb4V3P/pdb
EM Map EMD-2790: EMDB EMDataResource
NAKB: 4V3P

Classification: RIBOSOME
Organism(s): Triticum aestivum
Mutation(s): Yes

Deposited: 2014-10-20 Released: 2015-04-22
Deposition Author(s): Myasnikov, A.G., Afonina, Z.A., Menetret, J.F., Shirokov, V.A., Spirin, A.S., Klaholz, B.P.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 34.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

This is version 1.8 of the entry. See complete history.

Literature

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Myasnikov, A.G., Afonina, Z.A., Menetret, J.F., Shirokov, V.A., Spirin, A.S., Klaholz, B.P.

(2014) Nat Commun 5: 5294-5294

PubMed: 25376914 Search on PubMed
DOI: https://doi.org/10.1038/ncomms6294
Primary Citation of Related Structures:
4V3P

PubMed Abstract:
During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

Organizational Affiliation

1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France.

Macromolecule Content

Total Structure Weight: 3,001.44 kDa
Atom Count: 195,694
Modelled Residue Count: 16,504
Deposited Residue Count: 16,504
Unique protein chains: 78
Unique nucleic acid chains: 6

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G protein beta subunit	A [auth Sa]	380	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q8LNY6 (Triticum aestivum) Explore Q8LNY6 Go to UniProtKB: Q8LNY6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LNY6
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein SA	B [auth SA]	260	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative 40S ribosomal protein S3	C [auth SB]	208	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q8L804 (Triticum aestivum) Explore Q8L804 Go to UniProtKB: Q8L804
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8L804
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4	D [auth SD]	200	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S2	E [auth SE]	263	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	F [auth SF]	191	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S16	G [auth SI]	126	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S20	H [auth SJ]	128	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14	I [auth SK]	119	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23	J [auth SL]	142	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18	K [auth SM]	152	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13-1	L [auth SO]	121	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17-4	M [auth SQ]	141	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S11	N [auth SP]	85	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19	O [auth SS]	146	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S15	P [auth SR]	91	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25	Q [auth SV]	100	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S WHEAT GERM RIBOSOME1	R [auth SW]	92	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S28	S [auth SY]	58	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S30	T [auth SZ]	62	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 40S wheat germ ribosome protein 2	U [auth Sc]	25	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 40S wheat germ ribosome protein 3	V [auth Sb]	36	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 40S wheat germ ribosome protein 3	W [auth SU]	98	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S27	X [auth SX]	50	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9	Y [auth SC]	195	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 40S wheat germ ribosome protein 4	Z [auth SG]	143	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein S15	AA [auth SH]	130	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S29	BA [auth SN]	48	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K3 (Triticum aestivum) Explore Q5I7K3 Go to UniProtKB: Q5I7K3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K3
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S21	CA [auth ST]	82	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein	JA [auth LA]	216	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7L3 (Triticum aestivum) Explore Q5I7L3 Go to UniProtKB: Q5I7L3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7L3
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2	KA [auth LB]	255	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L11	LA [auth LE]	170	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7L2 (Triticum aestivum) Explore Q5I7L2 Go to UniProtKB: Q5I7L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7L2
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9	MA [auth LF]	190	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7a	NA [auth LH]	201	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal Pr 117	OA [auth LM]	140	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K4 (Triticum aestivum) Explore Q5I7K4 Go to UniProtKB: Q5I7K4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K4
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L15	PA [auth LP]	194	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27a-3	QA [auth LO]	144	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18	RA [auth LR]	163	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7L0 (Triticum aestivum) Explore Q5I7L0 Go to UniProtKB: Q5I7L0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7L0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	SA [auth LQ]	304	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L19	TA [auth LT]	189	Triticum aestivum	Mutation(s): 1
UniProt
Find proteins for Q7XY20 (Triticum aestivum) Explore Q7XY20 Go to UniProtKB: Q7XY20
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7XY20
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21	UA [auth LU]	164	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17	VA [auth LV]	171	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23a	WA [auth LX]	122	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24	XA [auth LZ]	75	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26	YA [auth LY]	130	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein l28	ZA [auth Lb]	73	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	AB [auth Ld]	23	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	BB [auth Lf]	112	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K9 (Triticum aestivum) Explore Q5I7K9 Go to UniProtKB: Q5I7K9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K9
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31	CB [auth Lg]	120	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal L32	DB [auth Lh]	133	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L37	EB [auth Ll]	94	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	FB [auth Ln]	69	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L39	GB [auth Lo]	51	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K7 (Triticum aestivum) Explore Q5I7K7 Go to UniProtKB: Q5I7K7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K7
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L44	HB [auth Lr]	105	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 60S wheat germ ribosome protein 1	IB [auth Lq]	25	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 60S wheat germ ribosome protein 2	JB [auth Ly], VB [auth Lx]	20	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 60S wheat germ ribosome protein 3	KB [auth Lz]	14	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6	LB [auth LG]	219	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7L4 (Triticum aestivum) Explore Q5I7L4 Go to UniProtKB: Q5I7L4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7L4
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 60S wheat germ ribosome protein 5	MB [auth LL]	182	Triticum aestivum	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown 60S wheat germ ribosome protein 6	NB [auth LN]	134	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18a	OB [auth LS]	167	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22	PB [auth LW]	108	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27	QB [auth La]	99	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein l34	RB [auth Li]	119	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K8 (Triticum aestivum) Explore Q5I7K8 Go to UniProtKB: Q5I7K8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K8
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
ribosomal protein L35A	SB [auth Lj]	104	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36	TB [auth Lk]	77	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7L5 (Triticum aestivum) Explore Q5I7L5 Go to UniProtKB: Q5I7L5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7L5
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-60S ribosomal protein L40-1	UB [auth Lp]	41	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L12	WB [auth LJ]	128	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein P1	XB [auth Lt], YB [auth Lu]	58	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K5 (Triticum aestivum) Explore Q5I7K5 Go to UniProtKB: Q5I7K5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K5
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
60S acidic ribosomal protein P2A	AC [auth Lw], ZB [auth Lv]	59	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for W5AP46 (Triticum aestivum) Explore W5AP46 Go to UniProtKB: W5AP46
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W5AP46
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35	BC [auth Lc]	124	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q8L805 (Triticum aestivum) Explore Q8L805 Go to UniProtKB: Q8L805
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8L805
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 78
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L7	CC [auth Le]	244	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7K6 (Triticum aestivum) Explore Q5I7K6 Go to UniProtKB: Q5I7K6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7K6
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 79
Molecule	Chains	Sequence Length	Organism	Details	Image
60S acidic ribosomal protein P0	DC [auth Ls]	262	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 80
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L3	EC [auth LC]	389	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q7X744 (Triticum aestivum) Explore Q7X744 Go to UniProtKB: Q7X744
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7X744
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 81
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4/L1	FC [auth LD]	372	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 82
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L13a	GC [auth LK]	206	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for Q5I7L1 (Triticum aestivum) Explore Q5I7L1 Go to UniProtKB: Q5I7L1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5I7L1
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 83
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37a, expressed	HC [auth Lm]	92	Triticum aestivum	Mutation(s): 0
UniProt
Find proteins for D8L9P6 (Triticum aestivum) Explore D8L9P6 Go to UniProtKB: D8L9P6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D8L9P6
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 84
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10-1	IC [auth LI]	184	Triticum aestivum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 34.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

EM Software:

Task	Software Package	Version
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	IMOD
RECONSTRUCTION	Xmipp

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-04-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-22
Type: Initial release
Version 1.1: 2016-12-14
Changes: Atomic model
Version 1.2: 2017-06-28
Changes: Data collection, Refinement description, Structure summary
Version 1.3: 2017-07-26
Changes: Database references, Structure summary
Version 1.4: 2017-08-23
Changes: Data collection, Derived calculations
Version 1.5: 2018-06-20
Changes: Advisory, Data collection, Database references, Derived calculations
Version 1.6: 2018-10-24
Changes: Advisory, Data collection, Derived calculations
Version 1.7: 2018-11-21
Changes: Advisory, Data collection, Derived calculations
Version 1.8: 2019-12-18
Changes: Other

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Entity ID: 30
Molecule	Chains	Length	Organism	Image
40S WHEAT GERM RIBOSOME protein 4	DA [auth S3]	11	Triticum aestivum
Sequence Annotations Expand
Reference Sequence LOADING

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 4V3P | pdb_00004v3p

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

Entity Groups

Sequence Annotations

Entity ID: 5

Entity Groups

Sequence Annotations

Entity ID: 6

Entity Groups

Sequence Annotations

Entity ID: 7

Entity Groups

Sequence Annotations

Entity ID: 8

Entity Groups

Sequence Annotations

Entity ID: 9

Entity Groups

Sequence Annotations

Entity ID: 10

Entity Groups

Sequence Annotations

Entity ID: 11

Entity Groups

Sequence Annotations

Entity ID: 12

Entity Groups

Sequence Annotations

Entity ID: 13

Entity Groups

Sequence Annotations

Entity ID: 14

Entity Groups

Sequence Annotations

Entity ID: 15

Entity Groups

Sequence Annotations

Entity ID: 16

Entity Groups

Sequence Annotations

Entity ID: 17

Entity Groups

Sequence Annotations

Entity ID: 18

Sequence Annotations

Entity ID: 19

Entity Groups

Sequence Annotations

Entity ID: 20

Entity Groups

Sequence Annotations

Entity ID: 21

Sequence Annotations

Entity ID: 22

Sequence Annotations

Entity ID: 23

Entity Groups

Sequence Annotations

Entity ID: 24

Entity Groups

Sequence Annotations

Entity ID: 25

Entity Groups

4V3P | pdb_00004v3p