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- PDB-10ic: Rhesus rotavirus (consensus structure at 4.7 Angstrom resolution ... -

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Basic information

Entry
Database: PDB / ID: 10ic
TitleRhesus rotavirus (consensus structure at 4.7 Angstrom resolution from cryo-ET)
Components
  • Inner capsid protein VP2
  • Intermediate capsid protein VP6
  • Outer capsid glycoprotein VP7
KeywordsVIRUS / Rotavirus / non-enveloped virus / viral entry / tomography
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / metal ion binding
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 / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesSimian rotavirus A strain RRV
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.7 Å
Authorsde Sautu, M. / Leistner, C. / Kirchhausen, T. / Jenni, S. / Harrison, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA13202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI163019 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanism of membrane perforation in rotavirus cell entry.
Authors: Marilina de Sautu / Conny Leistner / Tomas Kirchhausen / Simon Jenni / Stephen C Harrison
Abstract: Infectious cell entry by non-enveloped viruses requires delivery of the viral genome -- in many cases enclosed within a large, subviral particle -- across the membrane of an intracellular compartment. ...Infectious cell entry by non-enveloped viruses requires delivery of the viral genome -- in many cases enclosed within a large, subviral particle -- across the membrane of an intracellular compartment. Rotaviruses and other double-strand RNA (dsRNA) viruses introduce into their target cells an inner capsid particle, roughly 700 Å in diameter, that does not uncoat further but instead extrudes capped viral mRNA by virtue of RNA-dependent RNA polymerase and capping activities within it. The delivery agent is an outer protein layer of the virion. We describe here use of cryogenic electron tomography (cryo-ET) to visualize the full course of rhesus rotavirus (RRV) entry, from cell attachment and inward budding of the virion to arrival of the subviral particle in the cytosol. The cryo-tomograms and subtomogram averaging of classified subparticles have enabled us to link high-resolution structures of the virion and its components with time series from live-cell fluorescence microscopy and thus to outline the molecular mechanism of each step in the entry process, including the hitherto elusive membrane perforation step needed for transfer of the subviral particle into the cytosol.
History
DepositionJan 21, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data 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
Y: Outer capsid glycoprotein VP7
1: Outer capsid glycoprotein VP7
Z: Outer capsid glycoprotein VP7
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,280,457116
Polymers1,274,14328
Non-polymers6,31488
Water00
1
0: Outer capsid glycoprotein VP7
Y: Outer capsid glycoprotein VP7
1: Outer capsid glycoprotein VP7
Z: Outer capsid glycoprotein VP7
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
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)76,827,4396960
Polymers76,448,5761680
Non-polymers378,8635280
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
0: Outer capsid glycoprotein VP7
Y: Outer capsid glycoprotein VP7
1: Outer capsid glycoprotein VP7
Z: Outer capsid glycoprotein VP7
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
hetero molecules
x 5


  • icosahedral pentamer
  • 6.4 MDa, 140 polymers
Theoretical massNumber of molelcules
Total (without water)6,402,287580
Polymers6,370,715140
Non-polymers31,572440
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
0: Outer capsid glycoprotein VP7
Y: Outer capsid glycoprotein VP7
1: Outer capsid glycoprotein VP7
Z: Outer capsid glycoprotein VP7
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
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 7.68 MDa, 168 polymers
Theoretical massNumber of molelcules
Total (without water)7,682,744696
Polymers7,644,858168
Non-polymers37,886528
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 3 types, 28 molecules 0Y1ZPQRSTUVWXABCDEFGHIJKLMNO

#1: Protein
Outer capsid glycoprotein VP7


Mass: 37136.531 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet monkey) / References: UniProt: P12476
#2: 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 / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet monkey) / References: UniProt: B3F2X3
#3: Protein
Intermediate capsid protein VP6


Mass: 44962.773 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A strain RRV / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet monkey) / References: UniProt: B2BN53

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Sugars , 1 types, 13 molecules

#4: 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.: 13 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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, 75 molecules

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


Mass: 40.078 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Simian rotavirus A strain RRV / Type: VIRUS / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Simian rotavirus A strain RRV
Source (recombinant)Organism: Chlorocebus aethiops (grivet monkey) / Cell: MA104
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.3
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 3000 nm
Image recordingElectron dose: 3.8 e/Å2 / Avg electron dose per subtomogram: 156 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1Warpvolume selection
4WarpCTF correction
12Warp3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8565 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 537 / Num. of volumes extracted: 8565
Atomic model buildingProtocol: RIGID BODY FIT
Details: PDB-ID 9C1G placed without refinement. Position given by I2 point group symmetry.

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