[English] 日本語
Yorodumi
- PDB-8olc: SA11 Rotavirus Trypsinized Triple Layered Particle -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more