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234,440 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Keywords HAS EXACT PHRASE "Structural Protein/RNA"

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Search Summary

This query matches 39 Structures.

Refinements

Structure Determination Methodology

experimental (39)

Scientific Name of Source Organism

	Homo sapiens (6)
	Pseudomonas aeruginosa (6)
	Candidatus Scalindua brodae (5)
	Escherichia coli 'BL21-Gold(DE3)pLysS AG (4)
	Thermus thermophilus (4)
	Drosophila melanogaster (3)
	Geobacter sulfurreducens (3)
	Bombyx mori cypovirus 1 (2)
	Escherichia coli (2)
	synthetic construct (2)

More...

Taxonomy

	Bacteria (21)
	Eukaryota (13)
	Riboviria (4)
	other sequences (2)
	Archaea (1)

Experimental Method

	ELECTRON MICROSCOPY (22)
	X-RAY DIFFRACTION (14)
	SOLUTION NMR (3)

Polymer Entity Type

	Protein (39)
	RNA (35)
	DNA (8)

Refinement Resolution (Å)

	1.5 - 2.0 (1)
	2.0 - 2.5 (6)
	2.5 - 3.0 (13)
	3.0 - 3.5 (10)
	3.5 - 4.0 (1)
	4.0 - 4.5 (1)
	> 4.5 (4)

Release Date

	2000 - 2004 (4)
	2005 - 2009 (16)
	2010 - 2014 (1)
	2020 - 2024 (15)
	2025 - 2029 (3)

Enzyme Classification Name

Hydrolases (3)

Symmetry Type

	Asymmetric (32)
	Cyclic (5)
	Tetrahedral (3)

SCOP Classification

	Alpha and beta proteins (a+b) (11)
	Multi-domain proteins (alpha and beta) (2)
	All alpha proteins (2)
	Alpha and beta proteins (a/b) (2)
	Artifacts (1)
	Small proteins (1)

AllSelected

1 to 25 of 39 Structures

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1F6U \| pdb_00001f6u	Download File View File

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition

Amarasinghe, G.K., De Guzman, R.N., Turner, R.B., Chancellor, K.J., Summers, M.F.

(2000) J Mol Biology 301: 491-511

Released	2000-10-09
Method	SOLUTION NMR
Organisms	Human immunodeficiency virus 1
Macromolecule	HIV-1 NUCLEOCAPSID PROTEIN (protein) HIV-1 STEM-LOOP SL2 FROM PSI-RNA PACKAGING (nucleic acid)
Unique Ligands	ZN

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1FJE \| pdb_00001fje	Download File View File

SOLUTION STRUCTURE OF NUCLEOLIN RBD12 IN COMPLEX WITH SNRE RNA

Allain, F.H.T., Bouvet, P., Dieckmann, T., Feigon, J.

(2000) EMBO J 19: 6870-6881

Released	2001-01-03
Method	SOLUTION NMR
Organisms	Mesocricetus auratus
Macromolecule	NUCLEOLIN RBD12 (protein) SNRE RNA (nucleic acid)

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1RLG \| pdb_00001rlg	Download File View File

Molecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex

Moore, T., Zhang, Y., Fenley, M.O., Li, H.

(2004) Structure 12: 807-818

Released	2004-06-01
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Archaeoglobus fulgidus
Macromolecule	50S ribosomal protein L7Ae (protein) 25-MER (nucleic acid)

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1U6B \| pdb_00001u6b	Download File View File

CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS

Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J., Strobel, S.A.

(2004) Nature 430: 45-50

Released	2004-08-10
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Homo sapiens
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) 197-MER (nucleic acid) 5'-R(APAPGPCPCPAPCPAPCPAPAPAPCPCPAPGPAPCPGP GPCPC)-3' (nucleic acid) 5'-R(CPAP*(5MU))-3' (nucleic acid)
Unique Ligands	K, MG

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1X18 \| pdb_00001x18	Download File View File

Contact sites of ERA GTPase on the THERMUS THERMOPHILUS 30S SUBUNIT

Sharma, M.R., Barat, C., Agrawal, R.K.

(2005) Mol Cell 18: 319-329

Released	2005-05-17
Method	ELECTRON MICROSCOPY 13.5 Å
Organisms	Thermus thermophilus
Macromolecule	Unique protein chains: 5 Unique nucleic acid chains: 4

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1X1L \| pdb_00001x1l	Download File View File

Interaction of ERA,a GTPase protein, with the 3'minor domain of the 16S rRNA within the THERMUS THERMOPHILUS 30S subunit.

Sharma, M.R., Barat, C., Agrawal, R.K.

(2005) Mol Cell 18: 319-329

Released	2005-05-17
Method	ELECTRON MICROSCOPY 13.5 Å
Organisms	Escherichia coli Thermus thermophilus
Macromolecule	GTP-binding protein era (protein) RNA (130-MER) (nucleic acid)

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1Y39 \| pdb_00001y39	Download File View File

Co-evolution of protein and RNA structures within a highly conserved ribosomal domain

Dunstan, M.S., GuhaThakurta, D., Draper, D.E., Conn, G.L.

(2005) Chem Biol 12: 201-206

Released	2005-03-22
Method	X-RAY DIFFRACTION 2.8 Å
Organisms	Geobacillus stearothermophilus
Macromolecule	50S ribosomal protein L11 (protein) 58 Nucleotide Ribosomal 23S RNA Domain (nucleic acid)
Unique Ligands	3CO, GOL, K, MG

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1YSH \| pdb_00001ysh	Download File View File

Localization and dynamic behavior of ribosomal protein L30e

Halic, M., Becker, T., Frank, J., Spahn, C.M., Beckmann, R.

(2005) Nat Struct Mol Biol 12: 467-468

Released	2005-07-05
Method	ELECTRON MICROSCOPY 9.5 Å
Organisms	Oryza sativa Triticum aestivum synthetic construct
Macromolecule	Unique protein chains: 3 Unique nucleic acid chains: 3

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1ZHO \| pdb_00001zho	Download File View File

The structure of a ribosomal protein L1 in complex with mRNA

Nevskaya, N., Tishchenko, S., Volchkov, S., Kljashtorny, V., Nikonova, E., Nikonov, O., Nikulin, A., Kohrer, C., Piendl, W., Zimmermann, R., Stockley, P., Garber, M., Nikonov, S.

(2006) J Mol Biology 355: 747-759

Released	2006-05-09
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L1 (protein) mRNA (nucleic acid)
Unique Ligands	K

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1ZZN \| pdb_00001zzn	Download File View File

Crystal structure of a group I intron/two exon complex that includes all catalytic metal ion ligands.

Stahley, M.R., Strobel, S.A.

(2005) Science 309: 1587-1590

Released	2005-08-30
Method	X-RAY DIFFRACTION 3.37 Å
Organisms	Homo sapiens
Macromolecule	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A RNA BINDING DOMAIN (protein) 197-MER (nucleic acid) 5'-R(APAPGPCPCPAPCPAPCPAPAPAPCPCPAPGPAPCPGPGPCPC)-3' (nucleic acid) 5'-R(CPAP*(5MU))-3' (nucleic acid)
Unique Ligands	K, MG

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2FY1 \| pdb_00002fy1	Download File View File

A dual mode of RNA recognition by the RBMY protein

Skrisovska, L., Bourgois, C., Stefl, R., Kister, L., Wenter, P., Elliot, D., Stevenin, J., Allain, F.H.T.

(2007) EMBO Rep 8: 372-379

Released	2007-02-06
Method	SOLUTION NMR
Organisms	Homo sapiens synthetic construct
Macromolecule	RNA-binding motif protein, Y chromosome, family 1 member A1 (protein) S1A stem-loop RNA (nucleic acid)

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2HW8 \| pdb_00002hw8	Download File View File

Structure of ribosomal protein L1-mRNA complex at 2.1 resolution.

Tishchenko, S., Nikonova, E., Nikulin, A., Nevskaya, N., Volchkov, S., Piendl, W., Garber, M., Nikonov, S.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1545-1554

Released	2006-12-19
Method	X-RAY DIFFRACTION 2.1 Å
Organisms	Thermus thermophilus
Macromolecule	50S ribosomal protein L1 (protein) 36-MER (nucleic acid)
Unique Ligands	BU1, K, MG

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2NZ4 \| pdb_00002nz4	Download File View File

Structural investigation of the GlmS ribozyme bound to its catalytic cofactor

Cochrane, J.C.

(2007) Chem Biol 14: 97-105

Released	2007-01-16
Method	X-RAY DIFFRACTION 2.498 Å
Organisms	Homo sapiens
Macromolecule	U1 Small Nuclear Ribonucleoprotein A (protein) GlmS ribozyme (nucleic acid) substrate strand RNA 13-mer (nucleic acid)
Unique Ligands	GLP, MG

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2OIH \| pdb_00002oih	Download File View File

Hepatitis Delta Virus gemonic ribozyme precursor with C75U mutation and bound to monovalent cation Tl+

Ke, A., Ding, F., Batchelor, J.D., Doudna, J.A.

(2007) Structure 15: 281-287

Released	2007-03-27
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Homo sapiens
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) HDV ribozyme (nucleic acid)
Unique Ligands	TL

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2OJ3 \| pdb_00002oj3	Download File View File

Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)

Ke, A., Ding, F., Batchelor, J.D., Doudna, J.A.

(2007) Structure 15: 281-287

Released	2007-03-27
Method	X-RAY DIFFRACTION 2.9 Å
Organisms	Homo sapiens
Macromolecule	U1 small nuclear ribonucleoprotein A (protein) HDV RIBOZYME (nucleic acid)
Unique Ligands	NCO, TL

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2QUX \| pdb_00002qux	Download File View File

PP7 coat protein dimer in complex with RNA hairpin

Chao, J.A.

(2008) Nat Struct Mol Biol 15: 103-105

Released	2007-12-18
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Pseudomonas phage PP7
Macromolecule	Coat protein (protein) RNA (25-MER) (nucleic acid)
Unique Ligands	GOL

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7XG1 \| pdb_00007xg1	Download File View File

CryoEM structure of type IV-A Csf-crRNA binary complex

Zhang, J.T., Cui, N., Huang, H.D., Jia, N.

(2023) Mol Cell 83: 2493

Released	2023-08-02
Method	ELECTRON MICROSCOPY 3.3 Å
Organisms	Pseudomonas aeruginosa
Macromolecule	Csf1 (protein) Csf2 (protein) Csf3 (protein) crRNA (nucleic acid)
Unique Ligands	ZN

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7Y80 \| pdb_00007y80	Download File View File

CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA binary complex

Zhang, J.T., Cui, N., Huang, H.D., Jia, N.

(2022) Nat Commun 13: 7549-7549

Released	2022-12-14
Method	ELECTRON MICROSCOPY 2.71 Å
Organisms	Candidatus Scalindua brodae
Macromolecule	RAMP superfamily protein (protein) crRNA (nucleic acid)
Unique Ligands	MG, ZN

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7Y81 \| pdb_00007y81	Download File View File

CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA complex bound to non-self RNA target

Zhang, J.T., Cui, N., Huang, H.D., Jia, N.

(2022) Nat Commun 13: 7549-7549

Released	2022-12-14
Method	ELECTRON MICROSCOPY 2.54 Å
Organisms	Candidatus Scalindua brodae
Macromolecule	RAMP superfamily protein (protein) Non-self RNA target (nucleic acid) crRNA (nucleic acid)
Unique Ligands	MG, ZN

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7Y83 \| pdb_00007y83	Download File View File

CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in complex with TPR-CHAT protease bound to non-self RNA target

Zhang, J.T., Cui, N., Huang, H.D., Jia, N.

(2022) Nat Commun 13: 7549-7549

Released	2022-12-14
Method	ELECTRON MICROSCOPY 2.93 Å
Organisms	Candidatus Scalindua brodae
Macromolecule	CHAT domain protein (protein) RAMP superfamily protein (protein) crRNA (nucleic acid) non-self RNA (nucleic acid)
Unique Ligands	MG, ZN

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7Y84 \| pdb_00007y84	Download File View File

CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in complex with TPR-CHAT protease

Zhang, J.T., Cui, N., Huang, H.D., Jia, N.

(2022) Nat Commun 13: 7549-7549

Released	2022-12-14
Method	ELECTRON MICROSCOPY 2.61 Å
Organisms	Candidatus Scalindua brodae
Macromolecule	CHAT domain protein (protein) RAMP superfamily protein (protein) crRNA (nucleic acid)
Unique Ligands	MG, ZN

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7Y85 \| pdb_00007y85	Download File View File

CryoEM structure of type III-E CRISPR Craspase gRAMP-crRNA in complex with TPR-CHAT protease bound to self RNA target

Zhang, J.T., Cui, N., Huang, H.D., Jia, N.

(2022) Nat Commun 13: 7549-7549

Released	2022-12-14
Method	ELECTRON MICROSCOPY 2.73 Å
Organisms	Candidatus Scalindua brodae
Macromolecule	CHAT domain protein (protein) RAMP superfamily protein (protein) Self RNA target (nucleic acid) crRNA (nucleic acid)
Unique Ligands	MG, ZN

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8K34 \| pdb_00008k34	Download File View File

Cryo-EM structure of SPARTA gRNA binary complex

Zhang, J.T., Jia, N.

(2024) Nat Chem Biol 20: 503-511

Released	2024-01-17
Method	ELECTRON MICROSCOPY 2.81 Å
Organisms	Escherichia coli 'BL21-Gold(DE3)pLysS AG Thermoflavifilum thermophilum
Macromolecule	Piwi domain-containing protein (protein) TIR domain-containing protein (protein) RNA (5'-R(PAPAPAPCPGPGPCPUPCPUPAPAPUPCPUPAPUPUPAPGP*U)-3') (nucleic acid)
Unique Ligands	MG

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8YIG \| pdb_00008yig	Download File View File

DmDcr-2/LoqsPD/slm2 in initial binding state

Cao, N., Su, S., Wang, J., Ma, J., Wang, H.-W.

(2025) Nucleic Acids Res 53:

Released	2025-03-05
Method	ELECTRON MICROSCOPY 3.15 Å
Organisms	Drosophila melanogaster
Macromolecule	Dicer-2, isoform A (protein) Isoform PD of Protein Loquacious (protein) slm2 (nucleic acid)

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8YIH \| pdb_00008yih	Download File View File

DmDcr-2/LoqsPD/slm1 in pre-dicing state

Cao, N., Su, S., Wang, J., Ma, J., Wang, H.-W.

(2025) Nucleic Acids Res 53:

Released	2025-03-05
Method	ELECTRON MICROSCOPY 4.08 Å
Organisms	Drosophila melanogaster
Macromolecule	Dicer-2, isoform A (protein) Isoform PD of Protein Loquacious (protein) slm1 (nucleic acid)
Unique Ligands	ADP, MG

1 to 25 of 39 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1F6U | pdb_00001f6u

1FJE | pdb_00001fje

1RLG | pdb_00001rlg

1U6B | pdb_00001u6b

1X18 | pdb_00001x18

1X1L | pdb_00001x1l

1Y39 | pdb_00001y39

1YSH | pdb_00001ysh

1ZHO | pdb_00001zho

1ZZN | pdb_00001zzn

2FY1 | pdb_00002fy1

2HW8 | pdb_00002hw8

2NZ4 | pdb_00002nz4

2OIH | pdb_00002oih

2OJ3 | pdb_00002oj3

2QUX | pdb_00002qux

7XG1 | pdb_00007xg1

7Y80 | pdb_00007y80

7Y81 | pdb_00007y81

7Y83 | pdb_00007y83

7Y84 | pdb_00007y84

7Y85 | pdb_00007y85

8K34 | pdb_00008k34

8YIG | pdb_00008yig

8YIH | pdb_00008yih