[English] 日本語
- PDB-6j7v: Structure of HRPV6 VP5 fitted in the cryoEM density of the spike -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6j7v
TitleStructure of HRPV6 VP5 fitted in the cryoEM density of the spike
KeywordsVIRAL PROTEIN / HRPV6 / spike / envelope protein / fusion protein / archaea / haloarchaea
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / integral component of membrane / VP5
Function and homology information
Specimen sourceHalorubrum pleomorphic virus 6
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / 16 Å resolution
AuthorsEl Omari, K. / Li, S. / Huiskonen, J.T. / Stuart, D.I.
Funding supportUnited Kingdom , 1 items
OrganizationGrant numberCountry
European Research Council649053United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins.
Authors: Kamel El Omari / Sai Li / Abhay Kotecha / Thomas S Walter / Eduardo A Bignon / Karl Harlos / Pentti Somerharju / Felix De Haas / Daniel K Clare / Mika Molin / Felipe Hurtado / Mengqiu Li / Jonathan M Grimes / Dennis H Bamford / Nicole D Tischler / Juha T Huiskonen / David I Stuart / Elina Roine
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 18, 2019 / Release: Mar 6, 2019

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-9779
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9779
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: VP5

Theoretical massNumber of molelcules
Total (without water)57,3341

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein/peptide VP5

Mass: 57333.914 Da / Num. of mol.: 1 / Source: (natural) Halorubrum pleomorphic virus 6 / References: UniProt: H9ABP6

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: subtomogram averaging

Sample preparation

ComponentName: Halorubrum / Type: VIRUS / Entity ID: 1 / Source: NATURAL
Molecular weightValue: 0.057 MDa / Experimental value: NO
Source (natural)Organism: Halorubrum (archaea)
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Halorubrum
Virus shellName: Envelope
Buffer solutionpH: 7.2
Buffer componentConc.: 1.6 M / Name: sodium chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 1.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: Volta phase plate


EM software
7UCSF Chimeramodel fitting
10Dynamofinal Euler assignment
12Dynamo3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6057 / Symmetry type: POINT
EM volume selectionNumber of tomograms: 10 / Number of volumes extracted: 8953
Atomic model buildingRef protocol: RIGID BODY FIT / Target criteria: cross correlation
Atomic model buildingPDB-ID: 6QGL
Pdb chain ID: A

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at PDBe / 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. 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

Read more


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