9C1G | pdb_00009c1g

Rhesus rotavirus (consensus structure at 2.36 Angstrom resolution)

PDB DOI: https://doi.org/10.2210/pdb9C1G/pdb
EM Map EMD-45118: EMDB EMDataResource

Classification: VIRUS
Organism(s): Simian rotavirus A strain RRV
Expression System: Simian rotavirus A strain RRV
Mutation(s): No

Deposited: 2024-05-29 Released: 2025-04-30
Deposition Author(s): Jenni, S., Herrmann, T., De Sautu, M., Harrison, S.C.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9C1G

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

Literature

Rotavirus structure

Jenni, S., Herrmann, T., De Sautu, M., Harrison, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 1,280.46 kDa
Atom Count: 82,231
Modeled Residue Count: 10,269
Deposited Residue Count: 11,173
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer capsid glycoprotein VP7	A [auth 0] AA [auth Y] B [auth 1] BA [auth Z] R [auth P] A [auth 0], AA [auth Y], B [auth 1], BA [auth Z], R [auth P], S [auth Q], T [auth R], U [auth S], V [auth T], W [auth U], X [auth V], Y [auth W], Z [auth X]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12476
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth 0] Focus chain AA [auth Y] Focus chain B [auth 1] Focus chain BA [auth Z] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth S] Focus chain V [auth T] Focus chain W [auth U] Focus chain X [auth V] Focus chain Y [auth W] Focus chain Z [auth X]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner capsid protein VP2	C [auth A], D [auth B]	887	Simian rotavirus A strain RRV	Mutation(s): 0
UniProt
Find proteins for B3F2X3 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])) Explore B3F2X3 Go to UniProtKB: B3F2X3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3F2X3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Intermediate capsid protein VP6	E [auth C] F [auth D] G [auth E] H [auth F] I [auth G] E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N], Q [auth O]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2BN53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CA [auth 0] SDF format, chain CD [auth Y] SDF format, chain DC [auth T] SDF format, chain HD [auth Z] SDF format, chain IC [auth U] SDF format, chain JB [auth P] SDF format, chain NC [auth V] SDF format, chain OB [auth Q] SDF format, chain SC [auth W] SDF format, chain TB [auth R] SDF format, chain XC [auth X] SDF format, chain YB [auth S] SDF format, chain HA [auth 1] MOL2 format, chain CA [auth 0] MOL2 format, chain CD [auth Y] MOL2 format, chain DC [auth T] MOL2 format, chain HD [auth Z] MOL2 format, chain IC [auth U] MOL2 format, chain JB [auth P] MOL2 format, chain NC [auth V] MOL2 format, chain OB [auth Q] MOL2 format, chain SC [auth W] MOL2 format, chain TB [auth R] MOL2 format, chain XC [auth X] MOL2 format, chain YB [auth S] MOL2 format, chain HA [auth 1] mmCIF format, chain CA [auth 0] mmCIF format, chain CD [auth Y] mmCIF format, chain DC [auth T] mmCIF format, chain HD [auth Z] mmCIF format, chain IC [auth U] mmCIF format, chain JB [auth P] mmCIF format, chain NC [auth V] mmCIF format, chain OB [auth Q] mmCIF format, chain SC [auth W] mmCIF format, chain TB [auth R] mmCIF format, chain XC [auth X] mmCIF format, chain YB [auth S] mmCIF format, chain HA [auth 1]	CA [auth 0] CD [auth Y] DC [auth T] HA [auth 1] HD [auth Z] CA [auth 0], CD [auth Y], DC [auth T], HA [auth 1], HD [auth Z], IC [auth U], JB [auth P], NC [auth V], OB [auth Q], SC [auth W], TB [auth R], XC [auth X], YB [auth S]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth 0] Focus chain CD [auth Y] Focus chain DC [auth T] Focus chain HA [auth 1] Focus chain HD [auth Z] Focus chain IC [auth U] Focus chain JB [auth P] Focus chain NC [auth V] Focus chain OB [auth Q] Focus chain SC [auth W] Focus chain TB [auth R] Focus chain XC [auth X] Focus chain YB [auth S] Interactions & Density Focus chain CA [auth 0] Focus chain CD [auth Y] Focus chain DC [auth T] Focus chain HA [auth 1] Focus chain HD [auth Z] Focus chain IC [auth U] Focus chain JB [auth P] Focus chain NC [auth V] Focus chain OB [auth Q] Focus chain SC [auth W] Focus chain TB [auth R] Focus chain XC [auth X] Focus chain YB [auth S]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth L] SDF format, chain CB [auth L] SDF format, chain EB [auth M] SDF format, chain FB [auth N] SDF format, chain GB [auth O] SDF format, chain IB [auth O] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain QA [auth E] SDF format, chain RA [auth F] SDF format, chain TA [auth F] SDF format, chain UA [auth G] SDF format, chain VA [auth H] SDF format, chain WA [auth I] SDF format, chain YA [auth I] SDF format, chain ZA [auth J] SDF format, chain OA [auth D] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth L] MOL2 format, chain CB [auth L] MOL2 format, chain EB [auth M] MOL2 format, chain FB [auth N] MOL2 format, chain GB [auth O] MOL2 format, chain IB [auth O] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth H] MOL2 format, chain WA [auth I] MOL2 format, chain YA [auth I] MOL2 format, chain ZA [auth J] MOL2 format, chain OA [auth D] mmCIF format, chain AB [auth K] mmCIF format, chain BB [auth L] mmCIF format, chain CB [auth L] mmCIF format, chain EB [auth M] mmCIF format, chain FB [auth N] mmCIF format, chain GB [auth O] mmCIF format, chain IB [auth O] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth H] mmCIF format, chain WA [auth I] mmCIF format, chain YA [auth I] mmCIF format, chain ZA [auth J] mmCIF format, chain OA [auth D]	AB [auth K] BB [auth L] CB [auth L] EB [auth M] FB [auth N] AB [auth K], BB [auth L], CB [auth L], EB [auth M], FB [auth N], GB [auth O], IB [auth O], MA [auth C], NA [auth C], OA [auth D], QA [auth E], RA [auth F], TA [auth F], UA [auth G], VA [auth H], WA [auth I], YA [auth I], ZA [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain BB [auth L] Focus chain CB [auth L] Focus chain EB [auth M] Focus chain FB [auth N] Focus chain GB [auth O] Focus chain IB [auth O] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth D] Focus chain QA [auth E] Focus chain RA [auth F] Focus chain TA [auth F] Focus chain UA [auth G] Focus chain VA [auth H] Focus chain WA [auth I] Focus chain YA [auth I] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth K] Focus chain BB [auth L] Focus chain CB [auth L] Focus chain EB [auth M] Focus chain FB [auth N] Focus chain GB [auth O] Focus chain IB [auth O] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth D] Focus chain QA [auth E] Focus chain RA [auth F] Focus chain TA [auth F] Focus chain UA [auth G] Focus chain VA [auth H] Focus chain WA [auth I] Focus chain YA [auth I] Focus chain ZA [auth J]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AC [auth S] SDF format, chain AD [auth X] SDF format, chain BC [auth S] SDF format, chain BD [auth X] SDF format, chain CC [auth S] SDF format, chain DA [auth 0] SDF format, chain DD [auth Y] SDF format, chain EA [auth 0] SDF format, chain EC [auth T] SDF format, chain ED [auth Y] SDF format, chain FA [auth 0] SDF format, chain FC [auth T] SDF format, chain FD [auth Y] SDF format, chain GA [auth 0] SDF format, chain GC [auth T] SDF format, chain GD [auth Y] SDF format, chain HC [auth T] SDF format, chain IA [auth 1] SDF format, chain ID [auth Z] SDF format, chain JA [auth 1] SDF format, chain JC [auth U] SDF format, chain JD [auth Z] SDF format, chain KA [auth 1] SDF format, chain KB [auth P] SDF format, chain KD [auth Z] SDF format, chain LA [auth 1] SDF format, chain LB [auth P] SDF format, chain LC [auth U] SDF format, chain MB [auth P] SDF format, chain MC [auth U] SDF format, chain NB [auth P] SDF format, chain OC [auth V] SDF format, chain PB [auth Q] SDF format, chain PC [auth V] SDF format, chain QB [auth Q] SDF format, chain QC [auth V] SDF format, chain RB [auth Q] SDF format, chain RC [auth V] SDF format, chain SB [auth Q] SDF format, chain TC [auth W] SDF format, chain UB [auth R] SDF format, chain UC [auth W] SDF format, chain VB [auth R] SDF format, chain VC [auth W] SDF format, chain WB [auth R] SDF format, chain WC [auth W] SDF format, chain XB [auth R] SDF format, chain YC [auth X] SDF format, chain ZB [auth S] SDF format, chain ZC [auth X] SDF format, chain LD [auth Z] SDF format, chain KC [auth U] MOL2 format, chain AC [auth S] MOL2 format, chain AD [auth X] MOL2 format, chain BC [auth S] MOL2 format, chain BD [auth X] MOL2 format, chain CC [auth S] MOL2 format, chain DA [auth 0] MOL2 format, chain DD [auth Y] MOL2 format, chain EA [auth 0] MOL2 format, chain EC [auth T] MOL2 format, chain ED [auth Y] MOL2 format, chain FA [auth 0] MOL2 format, chain FC [auth T] MOL2 format, chain FD [auth Y] MOL2 format, chain GA [auth 0] MOL2 format, chain GC [auth T] MOL2 format, chain GD [auth Y] MOL2 format, chain HC [auth T] MOL2 format, chain IA [auth 1] MOL2 format, chain ID [auth Z] MOL2 format, chain JA [auth 1] MOL2 format, chain JC [auth U] MOL2 format, chain JD [auth Z] MOL2 format, chain KA [auth 1] MOL2 format, chain KB [auth P] MOL2 format, chain KD [auth Z] MOL2 format, chain LA [auth 1] MOL2 format, chain LB [auth P] MOL2 format, chain LC [auth U] MOL2 format, chain MB [auth P] MOL2 format, chain MC [auth U] MOL2 format, chain NB [auth P] MOL2 format, chain OC [auth V] MOL2 format, chain PB [auth Q] MOL2 format, chain PC [auth V] MOL2 format, chain QB [auth Q] MOL2 format, chain QC [auth V] MOL2 format, chain RB [auth Q] MOL2 format, chain RC [auth V] MOL2 format, chain SB [auth Q] MOL2 format, chain TC [auth W] MOL2 format, chain UB [auth R] MOL2 format, chain UC [auth W] MOL2 format, chain VB [auth R] MOL2 format, chain VC [auth W] MOL2 format, chain WB [auth R] MOL2 format, chain WC [auth W] MOL2 format, chain XB [auth R] MOL2 format, chain YC [auth X] MOL2 format, chain ZB [auth S] MOL2 format, chain ZC [auth X] MOL2 format, chain LD [auth Z] MOL2 format, chain KC [auth U] mmCIF format, chain AC [auth S] mmCIF format, chain AD [auth X] mmCIF format, chain BC [auth S] mmCIF format, chain BD [auth X] mmCIF format, chain CC [auth S] mmCIF format, chain DA [auth 0] mmCIF format, chain DD [auth Y] mmCIF format, chain EA [auth 0] mmCIF format, chain EC [auth T] mmCIF format, chain ED [auth Y] mmCIF format, chain FA [auth 0] mmCIF format, chain FC [auth T] mmCIF format, chain FD [auth Y] mmCIF format, chain GA [auth 0] mmCIF format, chain GC [auth T] mmCIF format, chain GD [auth Y] mmCIF format, chain HC [auth T] mmCIF format, chain IA [auth 1] mmCIF format, chain ID [auth Z] mmCIF format, chain JA [auth 1] mmCIF format, chain JC [auth U] mmCIF format, chain JD [auth Z] mmCIF format, chain KA [auth 1] mmCIF format, chain KB [auth P] mmCIF format, chain KD [auth Z] mmCIF format, chain LA [auth 1] mmCIF format, chain LB [auth P] mmCIF format, chain LC [auth U] mmCIF format, chain MB [auth P] mmCIF format, chain MC [auth U] mmCIF format, chain NB [auth P] mmCIF format, chain OC [auth V] mmCIF format, chain PB [auth Q] mmCIF format, chain PC [auth V] mmCIF format, chain QB [auth Q] mmCIF format, chain QC [auth V] mmCIF format, chain RB [auth Q] mmCIF format, chain RC [auth V] mmCIF format, chain SB [auth Q] mmCIF format, chain TC [auth W] mmCIF format, chain UB [auth R] mmCIF format, chain UC [auth W] mmCIF format, chain VB [auth R] mmCIF format, chain VC [auth W] mmCIF format, chain WB [auth R] mmCIF format, chain WC [auth W] mmCIF format, chain XB [auth R] mmCIF format, chain YC [auth X] mmCIF format, chain ZB [auth S] mmCIF format, chain ZC [auth X] mmCIF format, chain LD [auth Z] mmCIF format, chain KC [auth U]	AC [auth S] AD [auth X] BC [auth S] BD [auth X] CC [auth S] AC [auth S], AD [auth X], BC [auth S], BD [auth X], CC [auth S], DA [auth 0], DD [auth Y], EA [auth 0], EC [auth T], ED [auth Y], FA [auth 0], FC [auth T], FD [auth Y], GA [auth 0], GC [auth T], GD [auth Y], HC [auth T], IA [auth 1], ID [auth Z], JA [auth 1], JC [auth U], JD [auth Z], KA [auth 1], KB [auth P], KC [auth U], KD [auth Z], LA [auth 1], LB [auth P], LC [auth U], LD [auth Z], MB [auth P], MC [auth U], NB [auth P], OC [auth V], PB [auth Q], PC [auth V], QB [auth Q], QC [auth V], RB [auth Q], RC [auth V], SB [auth Q], TC [auth W], UB [auth R], UC [auth W], VB [auth R], VC [auth W], WB [auth R], WC [auth W], XB [auth R], YC [auth X], ZB [auth S], ZC [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AC [auth S] Focus chain AD [auth X] Focus chain BC [auth S] Focus chain BD [auth X] Focus chain CC [auth S] Focus chain DA [auth 0] Focus chain DD [auth Y] Focus chain EA [auth 0] Focus chain EC [auth T] Focus chain ED [auth Y] Focus chain FA [auth 0] Focus chain FC [auth T] Focus chain FD [auth Y] Focus chain GA [auth 0] Focus chain GC [auth T] Focus chain GD [auth Y] Focus chain HC [auth T] Focus chain IA [auth 1] Focus chain ID [auth Z] Focus chain JA [auth 1] Focus chain JC [auth U] Focus chain JD [auth Z] Focus chain KA [auth 1] Focus chain KB [auth P] Focus chain KC [auth U] Focus chain KD [auth Z] Focus chain LA [auth 1] Focus chain LB [auth P] Focus chain LC [auth U] Focus chain LD [auth Z] Focus chain MB [auth P] Focus chain MC [auth U] Focus chain NB [auth P] Focus chain OC [auth V] Focus chain PB [auth Q] Focus chain PC [auth V] Focus chain QB [auth Q] Focus chain QC [auth V] Focus chain RB [auth Q] Focus chain RC [auth V] Focus chain SB [auth Q] Focus chain TC [auth W] Focus chain UB [auth R] Focus chain UC [auth W] Focus chain VB [auth R] Focus chain VC [auth W] Focus chain WB [auth R] Focus chain WC [auth W] Focus chain XB [auth R] Focus chain YC [auth X] Focus chain ZB [auth S] Focus chain ZC [auth X] Interactions & Density Focus chain AC [auth S] Focus chain AD [auth X] Focus chain BC [auth S] Focus chain BD [auth X] Focus chain CC [auth S] Focus chain DA [auth 0] Focus chain DD [auth Y] Focus chain EA [auth 0] Focus chain EC [auth T] Focus chain ED [auth Y] Focus chain FA [auth 0] Focus chain FC [auth T] Focus chain FD [auth Y] Focus chain GA [auth 0] Focus chain GC [auth T] Focus chain GD [auth Y] Focus chain HC [auth T] Focus chain IA [auth 1] Focus chain ID [auth Z] Focus chain JA [auth 1] Focus chain JC [auth U] Focus chain JD [auth Z] Focus chain KA [auth 1] Focus chain KB [auth P] Focus chain KC [auth U] Focus chain KD [auth Z] Focus chain LA [auth 1] Focus chain LB [auth P] Focus chain LC [auth U] Focus chain LD [auth Z] Focus chain MB [auth P] Focus chain MC [auth U] Focus chain NB [auth P] Focus chain OC [auth V] Focus chain PB [auth Q] Focus chain PC [auth V] Focus chain QB [auth Q] Focus chain QC [auth V] Focus chain RB [auth Q] Focus chain RC [auth V] Focus chain SB [auth Q] Focus chain TC [auth W] Focus chain UB [auth R] Focus chain UC [auth W] Focus chain VB [auth R] Focus chain VC [auth W] Focus chain WB [auth R] Focus chain WC [auth W] Focus chain XB [auth R] Focus chain YC [auth X] Focus chain ZB [auth S] Focus chain ZC [auth X]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain DB [auth M] SDF format, chain HB [auth O] SDF format, chain PA [auth E] SDF format, chain SA [auth F] SDF format, chain XA [auth I] MOL2 format, chain DB [auth M] MOL2 format, chain HB [auth O] MOL2 format, chain PA [auth E] MOL2 format, chain SA [auth F] MOL2 format, chain XA [auth I] mmCIF format, chain DB [auth M] mmCIF format, chain HB [auth O] mmCIF format, chain PA [auth E] mmCIF format, chain SA [auth F] mmCIF format, chain XA [auth I]	DB [auth M], HB [auth O], PA [auth E], SA [auth F], XA [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DB [auth M] Focus chain HB [auth O] Focus chain PA [auth E] Focus chain SA [auth F] Focus chain XA [auth I] Interactions & Density Focus chain DB [auth M] Focus chain HB [auth O] Focus chain PA [auth E] Focus chain SA [auth F] Focus chain XA [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	E [auth C] F [auth D] G [auth E] H [auth F] I [auth G] E [auth C], F [auth D], G [auth E], H [auth F], I [auth G], J [auth H], K [auth I], L [auth J], M [auth K], N [auth L], O [auth M], P [auth N], Q [auth O]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21rc1_5127

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA13202

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.