9C1H | pdb_00009c1h

Rhesus rotavirus (upright structure at 2.88 Angstrom resolution)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9C1H

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: 2,036.37 kDa 
  • Atom Count: 130,385 
  • Modeled Residue Count: 16,328 
  • Deposited Residue Count: 17,839 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer capsid glycoprotein VP7326Simian rotavirus A strain RRVMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12476
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer capsid protein VP4C [auth 2],
D [auth 3],
E [auth 4]
776Simian rotavirus A strain RRVMutation(s): 0 
UniProt
Find proteins for P12473 (Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3]))
Explore P12473 
Go to UniProtKB:  P12473
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12473
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner capsid protein VP2F [auth A],
G [auth B]
887Simian rotavirus A strain RRVMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3F2X3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Intermediate capsid protein VP6397Simian rotavirus A strain RRVMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2BN53
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseRA [auth a]5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CD [auth V]
EC [auth Q]
EF [auth x]
JF [auth y]
KE [auth t]
CD [auth V],
EC [auth Q],
EF [auth x],
JF [auth y],
KE [auth t],
LD [auth X],
NC [auth S],
PE [auth u],
QD [auth Y],
SA [auth 0],
SC [auth T],
UE [auth v],
VD [auth Z],
XA [auth 1],
XC [auth U],
ZB [auth P],
ZE [auth w]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AE [auth f]
BE [auth f]
CB [auth C]
CE [auth g]
EB [auth C]
AE [auth f],
BE [auth f],
CB [auth C],
CE [auth g],
EB [auth C],
EE [auth h],
FB [auth D],
FE [auth i],
GB [auth E],
GE [auth i],
HB [auth F],
IE [auth j],
JB [auth F],
JE [auth k],
KB [auth G],
LB [auth H],
MB [auth I],
NB [auth I],
PB [auth J],
QB [auth K],
RB [auth L],
SB [auth L],
UB [auth M],
VB [auth N],
WB [auth O],
YB [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AB [auth 1]
AC [auth P]
AD [auth U]
AF [auth w]
BB [auth 1]
AB [auth 1],
AC [auth P],
AD [auth U],
AF [auth w],
BB [auth 1],
BC [auth P],
BD [auth U],
BF [auth w],
CC [auth P],
CF [auth w],
DC [auth P],
DD [auth V],
DF [auth w],
ED [auth V],
FC [auth Q],
FD [auth V],
FF [auth x],
GC [auth Q],
GD [auth V],
GF [auth x],
HC [auth Q],
HD [auth W],
HF [auth x],
IC [auth Q],
ID [auth W],
IF [auth x],
JC [auth R],
JD [auth W],
KC [auth R],
KD [auth W],
KF [auth y],
LC [auth R],
LE [auth t],
LF [auth y],
MC [auth R],
MD [auth X],
ME [auth t],
MF [auth y],
ND [auth X],
NE [auth t],
NF [auth y],
OC [auth S],
OD [auth X],
OE [auth t],
PC [auth S],
PD [auth X],
QC [auth S],
QE [auth u],
RC [auth S],
RD [auth Y],
RE [auth u],
SD [auth Y],
SE [auth u],
TA [auth 0],
TC [auth T],
TD [auth Y],
TE [auth u],
UA [auth 0],
UC [auth T],
UD [auth Y],
VA [auth 0],
VC [auth T],
VE [auth v],
WA [auth 0],
WC [auth T],
WD [auth Z],
WE [auth v],
XD [auth Z],
XE [auth v],
YA [auth 1],
YC [auth U],
YD [auth Z],
YE [auth v],
ZA [auth 1],
ZC [auth U],
ZD [auth Z]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
DB [auth C]
DE [auth h]
HE [auth j]
IB [auth F]
OB [auth J]
DB [auth C],
DE [auth h],
HE [auth j],
IB [auth F],
OB [auth J],
TB [auth M],
XB [auth O]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
FA [auth f]
GA [auth g]
H [auth C]
HA [auth h]
I [auth D]
FA [auth f],
GA [auth g],
H [auth C],
HA [auth h],
I [auth D],
IA [auth i],
J [auth E],
JA [auth j],
K [auth F],
KA [auth k],
L [auth G],
M [auth H],
N [auth I],
O [auth J],
P [auth K],
Q [auth L],
R [auth M],
S [auth N],
T [auth O]
L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA13202

Revision History  (Full details and data files)

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