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- PDB-8olc: SA11 Rotavirus Trypsinized Triple Layered Particle -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8olc
TitleSA11 Rotavirus Trypsinized Triple Layered Particle
Components
  • Inner capsid protein VP2
  • Intermediate capsid protein VP6
  • Outer capsid glycoprotein VP7
KeywordsVIRUS / Rotavirus / dsRNA virus
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / membrane / 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
Outer capsid glycoprotein VP7 / Inner capsid protein VP2 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesRotavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsAsensio-Cob, D. / Perez-Mata, C. / Gomez-Blanco, J. / Vargas, J. / Rodriguez, J.M. / Luque, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesISCIII-AESI PI20CIII/00014 Spain
CitationJournal: To Be Published
Title: Structural basis of rotavirus spike proteolytic activation
Authors: Asensio-Cob, D. / Perez-Mata, C. / Gomez-Blanco, J. / Vargas, J. / Rodriguez, J.M. / Luque, D.
History
DepositionMar 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
c: Outer capsid glycoprotein VP7
d: Outer capsid glycoprotein VP7
e: Outer capsid glycoprotein VP7
f: Outer capsid glycoprotein VP7
g: Outer capsid glycoprotein VP7
h: Outer capsid glycoprotein VP7
i: Outer capsid glycoprotein VP7
j: Outer capsid glycoprotein VP7
k: Outer capsid glycoprotein VP7
l: Outer capsid glycoprotein VP7
m: Outer capsid glycoprotein VP7
n: Outer capsid glycoprotein VP7
o: Outer capsid glycoprotein VP7
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
A: Inner capsid protein VP2
B: Inner capsid protein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,277,02169
Polymers1,273,44028
Non-polymers3,58141
Water00
1
c: Outer capsid glycoprotein VP7
d: Outer capsid glycoprotein VP7
e: Outer capsid glycoprotein VP7
f: Outer capsid glycoprotein VP7
g: Outer capsid glycoprotein VP7
h: Outer capsid glycoprotein VP7
i: Outer capsid glycoprotein VP7
j: Outer capsid glycoprotein VP7
k: Outer capsid glycoprotein VP7
l: Outer capsid glycoprotein VP7
m: Outer capsid glycoprotein VP7
n: Outer capsid glycoprotein VP7
o: Outer capsid glycoprotein VP7
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
A: Inner capsid protein VP2
B: Inner capsid protein VP2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)76,621,2834140
Polymers76,406,4141680
Non-polymers214,8692460
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59

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Components

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Protein , 3 types, 28 molecules cdefghijklmnoCDEFGHIJKLMNOAB

#1: Protein
Outer capsid glycoprotein VP7 / Inner capsid protein VP7


Mass: 37222.602 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Details: Outer capsid glycoprotein VP7 / Source: (gene. exp.) Rotavirus / Gene: VP7, VP1 / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A0A060IEQ1
#2: Protein
Intermediate capsid protein VP6 / Inner capsid protein VP6


Mass: 44910.738 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Details: Intermediate capsid protein VP6 / Source: (gene. exp.) Rotavirus / Gene: VP6 / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A2T3S6
#3: Protein Inner capsid protein VP2 / Inner core protein


Mass: 102853.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Inner core protein / Source: (gene. exp.) Rotavirus / Gene: VP2 / Cell line (production host): MA104 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: A2T3R1

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Sugars , 1 types, 10 molecules

#5: 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.: 10 / 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 , 2 types, 31 molecules

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


Mass: 40.078 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rotavirus A / Type: VIRUS / Details: Rotavirus SA11 Trypsinized TLP / Entity ID: #1-#3 / Source: NATURAL
Molecular weightValue: 92 MDa / Experimental value: NO
Source (natural)Organism: Rotavirus A / Strain: SA11
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Chlorocebus aethiops
Virus shellName: TLP / Diameter: 1000 nm
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295 K

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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 magnification: 58000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.9 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2368

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Processing

EM software
IDNameCategory
1Xmippparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 28427
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22394 / Symmetry type: POINT

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