[English] 日本語
Yorodumi
- PDB-4v7q: Atomic model of an infectious rotavirus particle -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 4v7q
TitleAtomic model of an infectious rotavirus particle
Components
  • Core scaffold protein
  • Intermediate capsid protein VP6
  • Outer capsid protein VP4
  • Outer layer protein VP7
KeywordsVIRUS / Rotavirus / Triple Layered Particle / Near Atomic Resolution / VP2 / VP6 / VP4 / VP7 / Double layered particle / de novo / Infectious / Virus / DLP / ICOSAHEDRAL VIRUS
Function / homologyHaemagglutinin outer capsid protein VP4, concanavalin-like domain / Rotavirus VP2 protein / Glycoprotein VP7 / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 helical domain / Concanavalin A-like lectin/glucanase domain superfamily / Viral capsid/haemagglutinin protein / Virus capsid protein, alpha-helical ...Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Rotavirus VP2 protein / Glycoprotein VP7 / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 helical domain / Concanavalin A-like lectin/glucanase domain superfamily / Viral capsid/haemagglutinin protein / Virus capsid protein, alpha-helical / Rotavirus VP2 / Glycoprotein VP7 / Rotavirus A/C, major capsid protein VP6 / Rotavirus VP4 membrane interaction domain / Rotavirus major capsid protein VP6 / Rotavirus VP4 helical domain / host cell endoplasmic reticulum lumen / viral intermediate capsid / T=13 icosahedral viral capsid / host cell rough endoplasmic reticulum / viral inner capsid / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral entry via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral nucleocapsid / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / membrane / metal ion binding / Intermediate capsid protein VP6 / Inner capsid protein VP2 / Outer capsid protein VP4 / Outer capsid glycoprotein VP7 / Outer capsid glycoprotein VP7
Function and homology information
Specimen sourceSimian rotavirus A
Rhesus rotavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsSettembre, E.C. / Chen, J.Z. / Dormitzer, P.R. / Grigorieff, N. / Harrison, S.C.
CitationJournal: EMBO J. / Year: 2011
Title: Atomic model of an infectious rotavirus particle.
Authors: Ethan C Settembre / James Z Chen / Philip R Dormitzer / Nikolaus Grigorieff / Stephen C Harrison
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 13, 2010 / Release: Jul 9, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 9, 2014Structure modelrepositoryInitial release
1.1Dec 10, 2014Structure modelOther
1.2Jan 24, 2018Structure modelData collection / Structure summaryaudit_author / em_image_scans_audit_author.name

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5199
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5199
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Core scaffold protein
AB: Core scaffold protein
AC: Intermediate capsid protein VP6
AD: Intermediate capsid protein VP6
AE: Intermediate capsid protein VP6
AF: Intermediate capsid protein VP6
AG: Intermediate capsid protein VP6
AH: Intermediate capsid protein VP6
AI: Intermediate capsid protein VP6
AJ: Intermediate capsid protein VP6
AK: Intermediate capsid protein VP6
AL: Intermediate capsid protein VP6
AM: Intermediate capsid protein VP6
AN: Intermediate capsid protein VP6
AO: Intermediate capsid protein VP6
BA: Outer layer protein VP7
BF: Outer layer protein VP7
BG: Outer layer protein VP7
BH: Outer layer protein VP7
BI: Outer layer protein VP7
BJ: Outer layer protein VP7
BK: Outer layer protein VP7
BL: Outer layer protein VP7
BM: Outer layer protein VP7
BN: Outer layer protein VP7
BO: Outer layer protein VP7
BP: Outer layer protein VP7
BQ: Outer layer protein VP7
BX: Outer capsid protein VP4
BY: Outer capsid protein VP4
BZ: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,440,16451
Polyers1,436,51931
Non-polymers3,64520
Water0
1
AA: Core scaffold protein
AB: Core scaffold protein
AC: Intermediate capsid protein VP6
AD: Intermediate capsid protein VP6
AE: Intermediate capsid protein VP6
AF: Intermediate capsid protein VP6
AG: Intermediate capsid protein VP6
AH: Intermediate capsid protein VP6
AI: Intermediate capsid protein VP6
AJ: Intermediate capsid protein VP6
AK: Intermediate capsid protein VP6
AL: Intermediate capsid protein VP6
AM: Intermediate capsid protein VP6
AN: Intermediate capsid protein VP6
AO: Intermediate capsid protein VP6
BA: Outer layer protein VP7
BF: Outer layer protein VP7
BG: Outer layer protein VP7
BH: Outer layer protein VP7
BI: Outer layer protein VP7
BJ: Outer layer protein VP7
BK: Outer layer protein VP7
BL: Outer layer protein VP7
BM: Outer layer protein VP7
BN: Outer layer protein VP7
BO: Outer layer protein VP7
BP: Outer layer protein VP7
BQ: Outer layer protein VP7
BX: Outer capsid protein VP4
BY: Outer capsid protein VP4
BZ: Outer capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)86,409,8453060
Polyers86,191,1351860
Non-polymers218,7101200
Water0
TypeNameSymmetry operationNumber
point symmetry operation60

-
Components

-
Protein/peptide , 4 types, 31 molecules AAABACADAEAFAGAHAIAJAKALAMANAOBABFBGBHBIBJBKBLBMBNBOBPBQBXBYBZ

#1: Protein/peptide Core scaffold protein / Core shell protein VP2


Mass: 93190.578 Da / Num. of mol.: 2 / Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Gene: Rotavirus / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B3F2X3
#2: Protein/peptide
Intermediate capsid protein VP6


Mass: 44934.766 Da / Num. of mol.: 13 / Source: (gene. exp.) Rhesus rotavirus / Strain: RRV / Gene: Rotavirus / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: B2BN53
#3: Protein/peptide
Outer layer protein VP7


Mass: 31232.234 Da / Num. of mol.: 13 / Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Cell (production host): KIDNEY CELLS / Organ (production host): KIDNEY / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: C3RX25, UniProt: P12476*PLUS
#4: Protein/peptide Outer capsid protein VP4


Mass: 86655.586 Da / Num. of mol.: 3 / Source: (gene. exp.) Simian rotavirus A / Strain: RRV / Cell (production host): KIDNEY CELLS / Organ (production host): KIDNEY / Production host: Chlorocebus sabaeus (green monkey) / References: UniProt: C3RX20

-
Non-polymers , 2 types, 20 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Formula: Zn / Zinc
#6: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 15 / Formula: C8H15NO6 / N-Acetylglucosamine

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsParent ID
1Rotavirus Triple Layered ParticleVIRUSThe sample was monodisperse0
2Rhesus Rotavirus (RRV) TLP1
Details of virusVirus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Macaca mulatta / Strain: Monkey Kidney Cells
Buffer solutionName: 20 mM Tris / Details: 20 mM Tris / pH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: in normal coldroom environment, ETHANE, manual plunger, front blotting for 3s before plunging, temperature 90 K

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F30 / Date: Mar 1, 2008
Details: Cut-plate film holders to reduce electron back-scattering
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Calibrated magnification: 56772 / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 90 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

CTF correctionDetails: individual particle
SymmetryPoint symmetry: I
3D reconstructionMethod: projection matching / Resolution: 3.8 Å / Number of particles: 4187 / Details: icosahedral (I2) averaging / Symmetry type: POINT
Number of atoms included #LASTProtein: 54043 / Nucleic acid: 0 / Ligand: 5 / Solvent: 0 / Total: 54048

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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