8QKM | pdb_00008qkm

Symmetric structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 gRNA

PDB DOI: https://doi.org/10.2210/pdb8QKM/pdb
EM Map EMD-18466: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Satellite tobacco necrosis virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-15 Released: 2025-03-26
Deposition Author(s): Javed, A., Mata, P.C., Stockley, P.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.39 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Virion assembly is regulated by sequence-specific and flexible genomic RNA-coat protein contacts

Wroblewski, E., Javed, A., Mata, P.C., Patel, N., Leonov, G., Philips, V.E.S., Twarock, R., Stockley, G.P.

To be published.

Macromolecule Content

Total Structure Weight: 1,249.68 kDa
Atom Count: 87,512
Modelled Residue Count: 11,280
Deposited Residue Count: 11,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A AA [auth a] AB [auth 0] B BA [auth b] A, AA [auth a], AB [auth 0], B, BA [auth b], BB [auth 1], C, CA [auth c], CB [auth 2], D, DA [auth d], DB [auth 3], E, EA [auth e], EB [auth 4], F, FA [auth f], FB [auth 5], G, GA [auth g], GB [auth 6], H, HA [auth h], HB [auth 7], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	188	Satellite tobacco necrosis virus 1	Mutation(s): 0
UniProt
Find proteins for P03606 (Satellite tobacco necrosis virus 1) Explore P03606 Go to UniProtKB: P03606
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03606
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain AC [auth K] SDF format, chain AD [auth a] SDF format, chain AE [auth w] SDF format, chain BC [auth K] SDF format, chain BD [auth b] SDF format, chain BE [auth x] SDF format, chain CC [auth L] SDF format, chain CD [auth c] SDF format, chain CE [auth y] SDF format, chain DC [auth M] SDF format, chain DD [auth d] SDF format, chain DE [auth y] SDF format, chain EC [auth M] SDF format, chain ED [auth e] SDF format, chain EE [auth z] SDF format, chain FC [auth N] SDF format, chain FD [auth f] SDF format, chain FE [auth 0] SDF format, chain GC [auth O] SDF format, chain GD [auth g] SDF format, chain GE [auth 0] SDF format, chain HC [auth O] SDF format, chain HD [auth h] SDF format, chain HE [auth 1] SDF format, chain IB [auth A] SDF format, chain IC [auth P] SDF format, chain ID [auth i] SDF format, chain IE [auth 1] SDF format, chain JB [auth A] SDF format, chain JC [auth P] SDF format, chain JD [auth i] SDF format, chain JE [auth 2] SDF format, chain KB [auth B] SDF format, chain KC [auth Q] SDF format, chain KD [auth j] SDF format, chain KE [auth 2] SDF format, chain LB [auth B] SDF format, chain LC [auth Q] SDF format, chain LD [auth k] SDF format, chain LE [auth 3] SDF format, chain MB [auth C] SDF format, chain MC [auth R] SDF format, chain MD [auth l] SDF format, chain ME [auth 3] SDF format, chain NB [auth D] SDF format, chain NC [auth R] SDF format, chain ND [auth m] SDF format, chain NE [auth 4] SDF format, chain OB [auth D] SDF format, chain OC [auth S] SDF format, chain OD [auth n] SDF format, chain OE [auth 4] SDF format, chain PB [auth E] SDF format, chain PC [auth S] SDF format, chain PD [auth o] SDF format, chain PE [auth 5] SDF format, chain QB [auth E] SDF format, chain QC [auth T] SDF format, chain QD [auth p] SDF format, chain QE [auth 5] SDF format, chain RB [auth F] SDF format, chain RC [auth U] SDF format, chain RD [auth q] SDF format, chain RE [auth 6] SDF format, chain SB [auth F] SDF format, chain SC [auth V] SDF format, chain SD [auth r] SDF format, chain SE [auth 6] SDF format, chain TB [auth G] SDF format, chain TC [auth W] SDF format, chain TD [auth s] SDF format, chain TE [auth 6] SDF format, chain UB [auth G] SDF format, chain UC [auth W] SDF format, chain UD [auth t] SDF format, chain UE [auth 7] SDF format, chain VB [auth H] SDF format, chain VC [auth X] SDF format, chain VD [auth t] SDF format, chain VE [auth 7] SDF format, chain WB [auth H] SDF format, chain WC [auth X] SDF format, chain WD [auth t] SDF format, chain XB [auth I] SDF format, chain XC [auth Y] SDF format, chain XD [auth u] SDF format, chain YB [auth I] SDF format, chain YC [auth Z] SDF format, chain YD [auth v] SDF format, chain ZB [auth J] SDF format, chain ZC [auth Z] SDF format, chain ZD [auth w] MOL2 format, chain AC [auth K] MOL2 format, chain AD [auth a] MOL2 format, chain AE [auth w] MOL2 format, chain BC [auth K] MOL2 format, chain BD [auth b] MOL2 format, chain BE [auth x] MOL2 format, chain CC [auth L] MOL2 format, chain CD [auth c] MOL2 format, chain CE [auth y] MOL2 format, chain DC [auth M] MOL2 format, chain DD [auth d] MOL2 format, chain DE [auth y] MOL2 format, chain EC [auth M] MOL2 format, chain ED [auth e] MOL2 format, chain EE [auth z] MOL2 format, chain FC [auth N] MOL2 format, chain FD [auth f] MOL2 format, chain FE [auth 0] MOL2 format, chain GC [auth O] MOL2 format, chain GD [auth g] MOL2 format, chain GE [auth 0] MOL2 format, chain HC [auth O] MOL2 format, chain HD [auth h] MOL2 format, chain HE [auth 1] MOL2 format, chain IB [auth A] MOL2 format, chain IC [auth P] MOL2 format, chain ID [auth i] MOL2 format, chain IE [auth 1] MOL2 format, chain JB [auth A] MOL2 format, chain JC [auth P] MOL2 format, chain JD [auth i] MOL2 format, chain JE [auth 2] MOL2 format, chain KB [auth B] MOL2 format, chain KC [auth Q] MOL2 format, chain KD [auth j] MOL2 format, chain KE [auth 2] MOL2 format, chain LB [auth B] MOL2 format, chain LC [auth Q] MOL2 format, chain LD [auth k] MOL2 format, chain LE [auth 3] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth R] MOL2 format, chain MD [auth l] MOL2 format, chain ME [auth 3] MOL2 format, chain NB [auth D] MOL2 format, chain NC [auth R] MOL2 format, chain ND [auth m] MOL2 format, chain NE [auth 4] MOL2 format, chain OB [auth D] MOL2 format, chain OC [auth S] MOL2 format, chain OD [auth n] MOL2 format, chain OE [auth 4] MOL2 format, chain PB [auth E] MOL2 format, chain PC [auth S] MOL2 format, chain PD [auth o] MOL2 format, chain PE [auth 5] MOL2 format, chain QB [auth E] MOL2 format, chain QC [auth T] MOL2 format, chain QD [auth p] MOL2 format, chain QE [auth 5] MOL2 format, chain RB [auth F] MOL2 format, chain RC [auth U] MOL2 format, chain RD [auth q] MOL2 format, chain RE [auth 6] MOL2 format, chain SB [auth F] MOL2 format, chain SC [auth V] MOL2 format, chain SD [auth r] MOL2 format, chain SE [auth 6] MOL2 format, chain TB [auth G] MOL2 format, chain TC [auth W] MOL2 format, chain TD [auth s] MOL2 format, chain TE [auth 6] MOL2 format, chain UB [auth G] MOL2 format, chain UC [auth W] MOL2 format, chain UD [auth t] MOL2 format, chain UE [auth 7] MOL2 format, chain VB [auth H] MOL2 format, chain VC [auth X] MOL2 format, chain VD [auth t] MOL2 format, chain VE [auth 7] MOL2 format, chain WB [auth H] MOL2 format, chain WC [auth X] MOL2 format, chain WD [auth t] MOL2 format, chain XB [auth I] MOL2 format, chain XC [auth Y] MOL2 format, chain XD [auth u] MOL2 format, chain YB [auth I] MOL2 format, chain YC [auth Z] MOL2 format, chain YD [auth v] MOL2 format, chain ZB [auth J] MOL2 format, chain ZC [auth Z] MOL2 format, chain ZD [auth w] mmCIF format, chain AC [auth K] mmCIF format, chain AD [auth a] mmCIF format, chain AE [auth w] mmCIF format, chain BC [auth K] mmCIF format, chain BD [auth b] mmCIF format, chain BE [auth x] mmCIF format, chain CC [auth L] mmCIF format, chain CD [auth c] mmCIF format, chain CE [auth y] mmCIF format, chain DC [auth M] mmCIF format, chain DD [auth d] mmCIF format, chain DE [auth y] mmCIF format, chain EC [auth M] mmCIF format, chain ED [auth e] mmCIF format, chain EE [auth z] mmCIF format, chain FC [auth N] mmCIF format, chain FD [auth f] mmCIF format, chain FE [auth 0] mmCIF format, chain GC [auth O] mmCIF format, chain GD [auth g] mmCIF format, chain GE [auth 0] mmCIF format, chain HC [auth O] mmCIF format, chain HD [auth h] mmCIF format, chain HE [auth 1] mmCIF format, chain IB [auth A] mmCIF format, chain IC [auth P] mmCIF format, chain ID [auth i] mmCIF format, chain IE [auth 1] mmCIF format, chain JB [auth A] mmCIF format, chain JC [auth P] mmCIF format, chain JD [auth i] mmCIF format, chain JE [auth 2] mmCIF format, chain KB [auth B] mmCIF format, chain KC [auth Q] mmCIF format, chain KD [auth j] mmCIF format, chain KE [auth 2] mmCIF format, chain LB [auth B] mmCIF format, chain LC [auth Q] mmCIF format, chain LD [auth k] mmCIF format, chain LE [auth 3] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth R] mmCIF format, chain MD [auth l] mmCIF format, chain ME [auth 3] mmCIF format, chain NB [auth D] mmCIF format, chain NC [auth R] mmCIF format, chain ND [auth m] mmCIF format, chain NE [auth 4] mmCIF format, chain OB [auth D] mmCIF format, chain OC [auth S] mmCIF format, chain OD [auth n] mmCIF format, chain OE [auth 4] mmCIF format, chain PB [auth E] mmCIF format, chain PC [auth S] mmCIF format, chain PD [auth o] mmCIF format, chain PE [auth 5] mmCIF format, chain QB [auth E] mmCIF format, chain QC [auth T] mmCIF format, chain QD [auth p] mmCIF format, chain QE [auth 5] mmCIF format, chain RB [auth F] mmCIF format, chain RC [auth U] mmCIF format, chain RD [auth q] mmCIF format, chain RE [auth 6] mmCIF format, chain SB [auth F] mmCIF format, chain SC [auth V] mmCIF format, chain SD [auth r] mmCIF format, chain SE [auth 6] mmCIF format, chain TB [auth G] mmCIF format, chain TC [auth W] mmCIF format, chain TD [auth s] mmCIF format, chain TE [auth 6] mmCIF format, chain UB [auth G] mmCIF format, chain UC [auth W] mmCIF format, chain UD [auth t] mmCIF format, chain UE [auth 7] mmCIF format, chain VB [auth H] mmCIF format, chain VC [auth X] mmCIF format, chain VD [auth t] mmCIF format, chain VE [auth 7] mmCIF format, chain WB [auth H] mmCIF format, chain WC [auth X] mmCIF format, chain WD [auth t] mmCIF format, chain XB [auth I] mmCIF format, chain XC [auth Y] mmCIF format, chain XD [auth u] mmCIF format, chain YB [auth I] mmCIF format, chain YC [auth Z] mmCIF format, chain YD [auth v] mmCIF format, chain ZB [auth J] mmCIF format, chain ZC [auth Z] mmCIF format, chain ZD [auth w]	AC [auth K] AD [auth a] AE [auth w] BC [auth K] BD [auth b] AC [auth K], AD [auth a], AE [auth w], BC [auth K], BD [auth b], BE [auth x], CC [auth L], CD [auth c], CE [auth y], DC [auth M], DD [auth d], DE [auth y], EC [auth M], ED [auth e], EE [auth z], FC [auth N], FD [auth f], FE [auth 0], GC [auth O], GD [auth g], GE [auth 0], HC [auth O], HD [auth h], HE [auth 1], IB [auth A], IC [auth P], ID [auth i], IE [auth 1], JB [auth A], JC [auth P], JD [auth i], JE [auth 2], KB [auth B], KC [auth Q], KD [auth j], KE [auth 2], LB [auth B], LC [auth Q], LD [auth k], LE [auth 3], MB [auth C], MC [auth R], MD [auth l], ME [auth 3], NB [auth D], NC [auth R], ND [auth m], NE [auth 4], OB [auth D], OC [auth S], OD [auth n], OE [auth 4], PB [auth E], PC [auth S], PD [auth o], PE [auth 5], QB [auth E], QC [auth T], QD [auth p], QE [auth 5], RB [auth F], RC [auth U], RD [auth q], RE [auth 6], SB [auth F], SC [auth V], SD [auth r], SE [auth 6], TB [auth G], TC [auth W], TD [auth s], TE [auth 6], UB [auth G], UC [auth W], UD [auth t], UE [auth 7], VB [auth H], VC [auth X], VD [auth t], VE [auth 7], WB [auth H], WC [auth X], WD [auth t], XB [auth I], XC [auth Y], XD [auth u], YB [auth I], YC [auth Z], YD [auth v], ZB [auth J], ZC [auth Z], ZD [auth w]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth K] Focus chain AD [auth a] Focus chain AE [auth w] Focus chain BC [auth K] Focus chain BD [auth b] Focus chain BE [auth x] Focus chain CC [auth L] Focus chain CD [auth c] Focus chain CE [auth y] Focus chain DC [auth M] Focus chain DD [auth d] Focus chain DE [auth y] Focus chain EC [auth M] Focus chain ED [auth e] Focus chain EE [auth z] Focus chain FC [auth N] Focus chain FD [auth f] Focus chain FE [auth 0] Focus chain GC [auth O] Focus chain GD [auth g] Focus chain GE [auth 0] Focus chain HC [auth O] Focus chain HD [auth h] Focus chain HE [auth 1] Focus chain IB [auth A] Focus chain IC [auth P] Focus chain ID [auth i] Focus chain IE [auth 1] Focus chain JB [auth A] Focus chain JC [auth P] Focus chain JD [auth i] Focus chain JE [auth 2] Focus chain KB [auth B] Focus chain KC [auth Q] Focus chain KD [auth j] Focus chain KE [auth 2] Focus chain LB [auth B] Focus chain LC [auth Q] Focus chain LD [auth k] Focus chain LE [auth 3] Focus chain MB [auth C] Focus chain MC [auth R] Focus chain MD [auth l] Focus chain ME [auth 3] Focus chain NB [auth D] Focus chain NC [auth R] Focus chain ND [auth m] Focus chain NE [auth 4] Focus chain OB [auth D] Focus chain OC [auth S] Focus chain OD [auth n] Focus chain OE [auth 4] Focus chain PB [auth E] Focus chain PC [auth S] Focus chain PD [auth o] Focus chain PE [auth 5] Focus chain QB [auth E] Focus chain QC [auth T] Focus chain QD [auth p] Focus chain QE [auth 5] Focus chain RB [auth F] Focus chain RC [auth U] Focus chain RD [auth q] Focus chain RE [auth 6] Focus chain SB [auth F] Focus chain SC [auth V] Focus chain SD [auth r] Focus chain SE [auth 6] Focus chain TB [auth G] Focus chain TC [auth W] Focus chain TD [auth s] Focus chain TE [auth 6] Focus chain UB [auth G] Focus chain UC [auth W] Focus chain UD [auth t] Focus chain UE [auth 7] Focus chain VB [auth H] Focus chain VC [auth X] Focus chain VD [auth t] Focus chain VE [auth 7] Focus chain WB [auth H] Focus chain WC [auth X] Focus chain WD [auth t] Focus chain XB [auth I] Focus chain XC [auth Y] Focus chain XD [auth u] Focus chain YB [auth I] Focus chain YC [auth Z] Focus chain YD [auth v] Focus chain ZB [auth J] Focus chain ZC [auth Z] Focus chain ZD [auth w] Interactions & Density Focus chain AC [auth K] Focus chain AD [auth a] Focus chain AE [auth w] Focus chain BC [auth K] Focus chain BD [auth b] Focus chain BE [auth x] Focus chain CC [auth L] Focus chain CD [auth c] Focus chain CE [auth y] Focus chain DC [auth M] Focus chain DD [auth d] Focus chain DE [auth y] Focus chain EC [auth M] Focus chain ED [auth e] Focus chain EE [auth z] Focus chain FC [auth N] Focus chain FD [auth f] Focus chain FE [auth 0] Focus chain GC [auth O] Focus chain GD [auth g] Focus chain GE [auth 0] Focus chain HC [auth O] Focus chain HD [auth h] Focus chain HE [auth 1] Focus chain IB [auth A] Focus chain IC [auth P] Focus chain ID [auth i] Focus chain IE [auth 1] Focus chain JB [auth A] Focus chain JC [auth P] Focus chain JD [auth i] Focus chain JE [auth 2] Focus chain KB [auth B] Focus chain KC [auth Q] Focus chain KD [auth j] Focus chain KE [auth 2] Focus chain LB [auth B] Focus chain LC [auth Q] Focus chain LD [auth k] Focus chain LE [auth 3] Focus chain MB [auth C] Focus chain MC [auth R] Focus chain MD [auth l] Focus chain ME [auth 3] Focus chain NB [auth D] Focus chain NC [auth R] Focus chain ND [auth m] Focus chain NE [auth 4] Focus chain OB [auth D] Focus chain OC [auth S] Focus chain OD [auth n] Focus chain OE [auth 4] Focus chain PB [auth E] Focus chain PC [auth S] Focus chain PD [auth o] Focus chain PE [auth 5] Focus chain QB [auth E] Focus chain QC [auth T] Focus chain QD [auth p] Focus chain QE [auth 5] Focus chain RB [auth F] Focus chain RC [auth U] Focus chain RD [auth q] Focus chain RE [auth 6] Focus chain SB [auth F] Focus chain SC [auth V] Focus chain SD [auth r] Focus chain SE [auth 6] Focus chain TB [auth G] Focus chain TC [auth W] Focus chain TD [auth s] Focus chain TE [auth 6] Focus chain UB [auth G] Focus chain UC [auth W] Focus chain UD [auth t] Focus chain UE [auth 7] Focus chain VB [auth H] Focus chain VC [auth X] Focus chain VD [auth t] Focus chain VE [auth 7] Focus chain WB [auth H] Focus chain WC [auth X] Focus chain WD [auth t] Focus chain XB [auth I] Focus chain XC [auth Y] Focus chain XD [auth u] Focus chain YB [auth I] Focus chain YC [auth Z] Focus chain YD [auth v] Focus chain ZB [auth J] Focus chain ZC [auth Z] Focus chain ZD [auth w]