[English] 日本語
Yorodumi
- EMDB-9779: Reconstruction of HRPV6 VP5 spike -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9779
TitleReconstruction of HRPV6 VP5 spike
Map data
Sample
  • Virus: Halorubrum (archaea)
    • Protein or peptide: VP5
KeywordsHRPV6 / spike / envelope protein / fusion protein / archaea / haloarchaea / VIRAL PROTEIN
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / membrane / VP5
Function and homology information
Biological speciesHalorubrum pleomorphic virus 6 / Halorubrum (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsLi S / Huiskonen JT
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
European Research Council649053 United 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 / ...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 /
Abstract: Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, ...Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
History
DepositionJan 18, 2019-
Header (metadata) releaseMar 6, 2019-
Map releaseMar 6, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6j7v
  • Surface level: 0.32
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j7v
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9779.png

Downloads & links

-
Map

FileDownload / File: emd_9779.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 128 pix.
= 286.72 Å		2.24 Å/pix.
x 128 pix.
= 286.72 Å		2.24 Å/pix.
x 128 pix.
= 286.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32 / Movie #1: 0.32
Minimum - Maximum-1.6049082 - 2.0089715
Average (Standard dev.)0.005550784 (±0.39763904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 286.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z286.720286.720286.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-1.6052.0090.006

-
Supplemental data

-
Mask #1

Fileemd_9779_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_9779_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_9779_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Halorubrum

EntireName: Halorubrum (archaea)
Components
  • Virus: Halorubrum (archaea)
    • Protein or peptide: VP5

-
Supramolecule #1: Halorubrum

SupramoleculeName: Halorubrum / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 56688 / Sci species name: Halorubrum / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Halorubrum (archaea)
Molecular weightTheoretical: 57 KDa
Virus shellShell ID: 1 / Name: Envelope

-
Macromolecule #1: VP5

MacromoleculeName: VP5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halorubrum pleomorphic virus 6
Molecular weightTheoretical: 57.333914 KDa
SequenceString: IAPLVGYAIG AAAISAVGGI GVGWTLREFE VVGSDDPAEG LTPDVLRNQL SDSVVKRKSN NQSTMVDNQN ILDGVEHTAY TEAKIAAIE ELNAGSSESA VLSAANSAID SYETTVRTNF YKSWNETVRE LEAMTQTVIA HADVGLSYIT DFGDPRFGNL A SGTSPNTL ...String:
IAPLVGYAIG AAAISAVGGI GVGWTLREFE VVGSDDPAEG LTPDVLRNQL SDSVVKRKSN NQSTMVDNQN ILDGVEHTAY TEAKIAAIE ELNAGSSESA VLSAANSAID SYETTVRTNF YKSWNETVRE LEAMTQTVIA HADVGLSYIT DFGDPRFGNL A SGTSPNTL KDTTVSMPDG TNFTLLTFRH NTGWDSGNAA YSVVEYNPKE VVTSTNSNTY NTVDGTQYMK FSEWNAVETE MD TVFQNVR NGISTWVTNV YGDVQSGAIE ISDLVTPRER ATMMAQEEGM SQAIADLIAL NVPVDAEREA TITIQDTGAT LPG TFALTD SSDGPLSAGQ TYDPSTFSGD VYFTADMSLV EGPWDAINSG VDGGTITITS EPYEGTAIEV TTVESETVSV PAAD WTDNG DGTWSYDASG DLETTITNVD SARFVSTATE TTYDTLQLKG AFTVDKLVNK QSGEEVSSTS FTSSEPQTDS NYITQ DEWD QLEQQNKELI EKYEQSQSGG GLDLGGLDMF GVPGEMVAVG AAAVIGFLML GNN

UniProtKB: VP5

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2 / Component - Concentration: 1.6 M / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 1.6 sec. / Average electron dose: 1.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 10 / Number images used: 8953
Final angle assignmentType: OTHER / Software - Name: Dynamo / Details: Sub-volume alignment
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 6057
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6qgl


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT / Target criteria: cross correlation
Output model

PDB-6j7v:
Structure of HRPV6 VP5 fitted in the cryoEM density of the spike

+
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://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