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- PDB-9c1h: Rhesus rotavirus (upright structure at 2.88 Angstrom resolution) -

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Basic information

Entry
Database: PDB / ID: 9c1h
TitleRhesus rotavirus (upright structure at 2.88 Angstrom resolution)
Components
  • (Outer capsid ...) x 2
  • Inner capsid protein VP2
  • Intermediate capsid protein VP6
KeywordsVIRAL PROTEIN / Rotavirus / non-enveloped virus / viral particle
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / host cell rough endoplasmic reticulum / T=2 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / T=13 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment ...viral intermediate capsid / host cell endoplasmic reticulum lumen / host cell rough endoplasmic reticulum / T=2 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / T=13 icosahedral viral capsid / viral inner capsid / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / metal ion binding / membrane
Similarity search - Function
Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain ...Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Viral capsid/haemagglutinin protein / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / Outer capsid protein VP4 / Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesSimian rotavirus A strain RRV
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsJenni, S. / Herrmann, T. / De Sautu, M. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA13202 United States
CitationJournal: To Be Published
Title: Rotavirus structure
Authors: Jenni, S. / Herrmann, T. / De Sautu, M. / Harrison, S.C.
History
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Outer capsid glycoprotein VP7
1: Outer capsid glycoprotein VP7
2: Outer capsid protein VP4
3: Outer capsid protein VP4
4: Outer capsid protein VP4
A: Inner capsid protein VP2
B: Inner capsid protein VP2
C: Intermediate capsid protein VP6
D: Intermediate capsid protein VP6
E: Intermediate capsid protein VP6
F: Intermediate capsid protein VP6
G: Intermediate capsid protein VP6
H: Intermediate capsid protein VP6
I: Intermediate capsid protein VP6
J: Intermediate capsid protein VP6
K: Intermediate capsid protein VP6
L: Intermediate capsid protein VP6
M: Intermediate capsid protein VP6
N: Intermediate capsid protein VP6
O: Intermediate capsid protein VP6
P: Outer capsid glycoprotein VP7
Q: Outer capsid glycoprotein VP7
R: Outer capsid glycoprotein VP7
S: Outer capsid glycoprotein VP7
T: Outer capsid glycoprotein VP7
U: Outer capsid glycoprotein VP7
V: Outer capsid glycoprotein VP7
W: Outer capsid glycoprotein VP7
X: Outer capsid glycoprotein VP7
Y: Outer capsid glycoprotein VP7
Z: Outer capsid glycoprotein VP7
f: Intermediate capsid protein VP6
g: Intermediate capsid protein VP6
h: Intermediate capsid protein VP6
i: Intermediate capsid protein VP6
j: Intermediate capsid protein VP6
k: Intermediate capsid protein VP6
t: Outer capsid glycoprotein VP7
u: Outer capsid glycoprotein VP7
v: Outer capsid glycoprotein VP7
w: Outer capsid glycoprotein VP7
x: Outer capsid glycoprotein VP7
y: Outer capsid glycoprotein VP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,036,372170
Polymers2,026,70643
Non-polymers9,666127
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Outer capsid ... , 2 types, 22 molecules 01PQRSTUVWXYZtuvwxy234

#1: Protein
Outer capsid glycoprotein VP7


Mass: 37136.531 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Production host: Simian rotavirus A strain RRV / References: UniProt: P12476
#2: Protein Outer capsid protein VP4 / Hemagglutinin


Mass: 86655.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Production host: Simian rotavirus A strain RRV / References: UniProt: P12473

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Protein , 2 types, 21 molecules ABCDEFGHIJKLMNOfghijk

#3: Protein Inner capsid protein VP2 / VP2A


Mass: 103425.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Production host: Simian rotavirus A strain RRV / References: UniProt: B3F2X3
#4: Protein
Intermediate capsid protein VP6


Mass: 44962.773 Da / Num. of mol.: 19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Production host: Simian rotavirus A strain RRV / References: UniProt: B2BN53

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Sugars , 2 types, 18 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 109 molecules

#7: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: Ca
#8: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Zn
#9: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Simian rotavirus A strain RRV / Type: VIRUS / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Simian rotavirus A strain RRV
Source (recombinant)Organism: Simian rotavirus A strain RRV
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5127 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 542965 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 60.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034133016
ELECTRON MICROSCOPYf_angle_d0.5445181125
ELECTRON MICROSCOPYf_chiral_restr0.041420822
ELECTRON MICROSCOPYf_plane_restr0.004123406
ELECTRON MICROSCOPYf_dihedral_angle_d4.741617764

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