6WXG

Cryo-EM reconstruction of VP5/VP8 assembly from rhesus rotavirus particles - Reversed conformation

PDB DOI: https://doi.org/10.2210/pdb6WXG/pdb
EM Map EMD-21957: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Simian rotavirus A strain RRV
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2020-05-10 Released: 2021-01-20
Deposition Author(s): Herrmann, T., Harrison, S.C., Jenni, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 1,743.4 kDa
Atom Count: 101,709
Modelled Residue Count: 12,763
Deposited Residue Count: 15,342
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid protein VP4	A [auth 1], B [auth 2], C [auth 3]	776	Simian rotavirus A strain RRV	Mutation(s): 0
UniProt
Find proteins for G0YZG6 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore G0YZG6 Go to UniProtKB: G0YZG6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0YZG6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermediate capsid protein VP6	D [auth A] E [auth B] F [auth C] G [auth D] H [auth E] D [auth A], E [auth B], F [auth C], G [auth D], H [auth E], I [auth F], J [auth G], K [auth H], L [auth I], M [auth J], N [auth K], O [auth L], P [auth M], Q [auth N], R [auth O], S [auth P], T [auth Q], U [auth R]	397	Simian rotavirus A strain RRV	Mutation(s): 0
UniProt
Find proteins for B2BN53 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore B2BN53 Go to UniProtKB: B2BN53
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B2BN53
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid glycoprotein VP7	AA [auth f] BA [auth g] CA [auth h] DA [auth i] EA [auth j] AA [auth f], BA [auth g], CA [auth h], DA [auth i], EA [auth j], FA [auth k], GA [auth l], HA [auth m], IA [auth n], JA [auth o], KA [auth p], LA [auth q], MA [auth r], V [auth a], W [auth b], X [auth c], Y [auth d], Z [auth e]	326	Simian rotavirus A strain RRV	Mutation(s): 0
UniProt
Find proteins for P12476 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore P12476 Go to UniProtKB: P12476
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12476
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain DC [auth k] SDF format, chain FB [auth e] SDF format, chain LB [auth g] SDF format, chain PC [auth n] SDF format, chain TA [auth b] SDF format, chain VC [auth p] SDF format, chain XA [auth c] SDF format, chain BD [auth q] SDF format, chain FD [auth r] SDF format, chain HC [auth l] SDF format, chain JB [auth f] SDF format, chain JC [auth m] SDF format, chain NA [auth a] SDF format, chain RB [auth h] SDF format, chain TC [auth o] SDF format, chain VB [auth i] SDF format, chain XB [auth j] SDF format, chain ZA [auth d] MOL2 format, chain DC [auth k] MOL2 format, chain FB [auth e] MOL2 format, chain LB [auth g] MOL2 format, chain PC [auth n] MOL2 format, chain TA [auth b] MOL2 format, chain VC [auth p] MOL2 format, chain XA [auth c] MOL2 format, chain BD [auth q] MOL2 format, chain FD [auth r] MOL2 format, chain HC [auth l] MOL2 format, chain JB [auth f] MOL2 format, chain JC [auth m] MOL2 format, chain NA [auth a] MOL2 format, chain RB [auth h] MOL2 format, chain TC [auth o] MOL2 format, chain VB [auth i] MOL2 format, chain XB [auth j] MOL2 format, chain ZA [auth d]	BD [auth q] DC [auth k] FB [auth e] FD [auth r] HC [auth l] BD [auth q], DC [auth k], FB [auth e], FD [auth r], HC [auth l], JB [auth f], JC [auth m], LB [auth g], NA [auth a], PC [auth n], RB [auth h], TA [auth b], TC [auth o], VB [auth i], VC [auth p], XA [auth c], XB [auth j], ZA [auth d]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BD [auth q] Focus chain DC [auth k] Focus chain FB [auth e] Focus chain FD [auth r] Focus chain HC [auth l] Focus chain JB [auth f] Focus chain JC [auth m] Focus chain LB [auth g] Focus chain NA [auth a] Focus chain PC [auth n] Focus chain RB [auth h] Focus chain TA [auth b] Focus chain TC [auth o] Focus chain VB [auth i] Focus chain VC [auth p] Focus chain XA [auth c] Focus chain XB [auth j] Focus chain ZA [auth d] Interactions & Density Focus chain BD [auth q] Focus chain DC [auth k] Focus chain FB [auth e] Focus chain FD [auth r] Focus chain HC [auth l] Focus chain JB [auth f] Focus chain JC [auth m] Focus chain LB [auth g] Focus chain NA [auth a] Focus chain PC [auth n] Focus chain RB [auth h] Focus chain TA [auth b] Focus chain TC [auth o] Focus chain VB [auth i] Focus chain VC [auth p] Focus chain XA [auth c] Focus chain XB [auth j] Focus chain ZA [auth d]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AC [auth j] SDF format, chain AD [auth p] SDF format, chain BB [auth d] SDF format, chain CB [auth d] SDF format, chain CC [auth j] SDF format, chain CD [auth q] SDF format, chain DB [auth d] SDF format, chain ED [auth q] SDF format, chain FC [auth k] SDF format, chain GC [auth k] SDF format, chain GD [auth r] SDF format, chain IC [auth l] SDF format, chain KC [auth m] SDF format, chain MC [auth m] SDF format, chain NB [auth g] SDF format, chain NC [auth m] SDF format, chain OC [auth m] SDF format, chain PB [auth g] SDF format, chain QB [auth g] SDF format, chain QC [auth n] SDF format, chain RC [auth n] SDF format, chain SA [auth a] SDF format, chain SB [auth h] SDF format, chain SC [auth n] SDF format, chain AB [auth d] SDF format, chain BC [auth j] SDF format, chain DD [auth q] SDF format, chain EB [auth d] SDF format, chain EC [auth k] SDF format, chain GB [auth e] SDF format, chain HB [auth e] SDF format, chain IB [auth e] SDF format, chain KB [auth f] SDF format, chain LC [auth m] SDF format, chain MB [auth g] SDF format, chain OA [auth a] SDF format, chain OB [auth g] SDF format, chain PA [auth a] SDF format, chain QA [auth a] SDF format, chain RA [auth a] SDF format, chain TB [auth h] SDF format, chain UA [auth b] SDF format, chain UB [auth h] SDF format, chain UC [auth o] SDF format, chain VA [auth b] SDF format, chain WA [auth b] SDF format, chain WB [auth i] SDF format, chain WC [auth p] SDF format, chain XC [auth p] SDF format, chain YA [auth c] SDF format, chain YB [auth j] SDF format, chain YC [auth p] SDF format, chain ZB [auth j] SDF format, chain ZC [auth p] MOL2 format, chain AC [auth j] MOL2 format, chain AD [auth p] MOL2 format, chain BB [auth d] MOL2 format, chain CB [auth d] MOL2 format, chain CC [auth j] MOL2 format, chain CD [auth q] MOL2 format, chain DB [auth d] MOL2 format, chain ED [auth q] MOL2 format, chain FC [auth k] MOL2 format, chain GC [auth k] MOL2 format, chain GD [auth r] MOL2 format, chain IC [auth l] MOL2 format, chain KC [auth m] MOL2 format, chain MC [auth m] MOL2 format, chain NB [auth g] MOL2 format, chain NC [auth m] MOL2 format, chain OC [auth m] MOL2 format, chain PB [auth g] MOL2 format, chain QB [auth g] MOL2 format, chain QC [auth n] MOL2 format, chain RC [auth n] MOL2 format, chain SA [auth a] MOL2 format, chain SB [auth h] MOL2 format, chain SC [auth n] MOL2 format, chain AB [auth d] MOL2 format, chain BC [auth j] MOL2 format, chain DD [auth q] MOL2 format, chain EB [auth d] MOL2 format, chain EC [auth k] MOL2 format, chain GB [auth e] MOL2 format, chain HB [auth e] MOL2 format, chain IB [auth e] MOL2 format, chain KB [auth f] MOL2 format, chain LC [auth m] MOL2 format, chain MB [auth g] MOL2 format, chain OA [auth a] MOL2 format, chain OB [auth g] MOL2 format, chain PA [auth a] MOL2 format, chain QA [auth a] MOL2 format, chain RA [auth a] MOL2 format, chain TB [auth h] MOL2 format, chain UA [auth b] MOL2 format, chain UB [auth h] MOL2 format, chain UC [auth o] MOL2 format, chain VA [auth b] MOL2 format, chain WA [auth b] MOL2 format, chain WB [auth i] MOL2 format, chain WC [auth p] MOL2 format, chain XC [auth p] MOL2 format, chain YA [auth c] MOL2 format, chain YB [auth j] MOL2 format, chain YC [auth p] MOL2 format, chain ZB [auth j] MOL2 format, chain ZC [auth p]	AB [auth d] AC [auth j] AD [auth p] BB [auth d] BC [auth j] AB [auth d], AC [auth j], AD [auth p], BB [auth d], BC [auth j], CB [auth d], CC [auth j], CD [auth q], DB [auth d], DD [auth q], EB [auth d], EC [auth k], ED [auth q], FC [auth k], GB [auth e], GC [auth k], GD [auth r], HB [auth e], IB [auth e], IC [auth l], KB [auth f], KC [auth m], LC [auth m], MB [auth g], MC [auth m], NB [auth g], NC [auth m], OA [auth a], OB [auth g], OC [auth m], PA [auth a], PB [auth g], QA [auth a], QB [auth g], QC [auth n], RA [auth a], RC [auth n], SA [auth a], SB [auth h], SC [auth n], TB [auth h], UA [auth b], UB [auth h], UC [auth o], VA [auth b], WA [auth b], WB [auth i], WC [auth p], XC [auth p], YA [auth c], YB [auth j], YC [auth p], ZB [auth j], ZC [auth p]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AB [auth d] Focus chain AC [auth j] Focus chain AD [auth p] Focus chain BB [auth d] Focus chain BC [auth j] Focus chain CB [auth d] Focus chain CC [auth j] Focus chain CD [auth q] Focus chain DB [auth d] Focus chain DD [auth q] Focus chain EB [auth d] Focus chain EC [auth k] Focus chain ED [auth q] Focus chain FC [auth k] Focus chain GB [auth e] Focus chain GC [auth k] Focus chain GD [auth r] Focus chain HB [auth e] Focus chain IB [auth e] Focus chain IC [auth l] Focus chain KB [auth f] Focus chain KC [auth m] Focus chain LC [auth m] Focus chain MB [auth g] Focus chain MC [auth m] Focus chain NB [auth g] Focus chain NC [auth m] Focus chain OA [auth a] Focus chain OB [auth g] Focus chain OC [auth m] Focus chain PA [auth a] Focus chain PB [auth g] Focus chain QA [auth a] Focus chain QB [auth g] Focus chain QC [auth n] Focus chain RA [auth a] Focus chain RC [auth n] Focus chain SA [auth a] Focus chain SB [auth h] Focus chain SC [auth n] Focus chain TB [auth h] Focus chain UA [auth b] Focus chain UB [auth h] Focus chain UC [auth o] Focus chain VA [auth b] Focus chain WA [auth b] Focus chain WB [auth i] Focus chain WC [auth p] Focus chain XC [auth p] Focus chain YA [auth c] Focus chain YB [auth j] Focus chain YC [auth p] Focus chain ZB [auth j] Focus chain ZC [auth p] Interactions & Density Focus chain AB [auth d] Focus chain AC [auth j] Focus chain AD [auth p] Focus chain BB [auth d] Focus chain BC [auth j] Focus chain CB [auth d] Focus chain CC [auth j] Focus chain CD [auth q] Focus chain DB [auth d] Focus chain DD [auth q] Focus chain EB [auth d] Focus chain EC [auth k] Focus chain ED [auth q] Focus chain FC [auth k] Focus chain GB [auth e] Focus chain GC [auth k] Focus chain GD [auth r] Focus chain HB [auth e] Focus chain IB [auth e] Focus chain IC [auth l] Focus chain KB [auth f] Focus chain KC [auth m] Focus chain LC [auth m] Focus chain MB [auth g] Focus chain MC [auth m] Focus chain NB [auth g] Focus chain NC [auth m] Focus chain OA [auth a] Focus chain OB [auth g] Focus chain OC [auth m] Focus chain PA [auth a] Focus chain PB [auth g] Focus chain QA [auth a] Focus chain QB [auth g] Focus chain QC [auth n] Focus chain RA [auth a] Focus chain RC [auth n] Focus chain SA [auth a] Focus chain SB [auth h] Focus chain SC [auth n] Focus chain TB [auth h] Focus chain UA [auth b] Focus chain UB [auth h] Focus chain UC [auth o] Focus chain VA [auth b] Focus chain WA [auth b] Focus chain WB [auth i] Focus chain WC [auth p] Focus chain XC [auth p] Focus chain YA [auth c] Focus chain YB [auth j] Focus chain YC [auth p] Focus chain ZB [auth j] Focus chain ZC [auth p]