[English] 日本語
Yorodumi
- EMDB-6387: A new view of essential vertex proteins on herpesvirus capsids ob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6387
TitleA new view of essential vertex proteins on herpesvirus capsids observed inside intact virions
Map dataReconstruction of pseudorabies virus capsid imaged inside virions
Sample
  • Sample: Capsid of pseudorabies virus imaged in intact virions
  • Virus: Suid herpesvirus 1
KeywordsPseudorabies virus / PRV / capsid / virion / CVSC / pUL17 / pUL25 / pUL36
Biological speciesSuid herpesvirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsHuet A / Makhov AM / Huffman JB / Vos M / Homa FL / Conway JF
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Extensive subunit contacts underpin herpesvirus capsid stability and interior-to-exterior allostery.
Authors: Alexis Huet / Alexander M Makhov / Jamie B Huffman / Matthijn Vos / Fred L Homa / James F Conway /
Abstract: The herpesvirus capsid is a complex protein assembly that includes hundreds of copies of four major subunits and lesser numbers of several minor proteins, all of which are essential for infectivity. ...The herpesvirus capsid is a complex protein assembly that includes hundreds of copies of four major subunits and lesser numbers of several minor proteins, all of which are essential for infectivity. Cryo-electron microscopy is uniquely suited for studying interactions that govern the assembly and function of such large functional complexes. Here we report two high-quality capsid structures, from human herpes simplex virus type 1 (HSV-1) and the animal pseudorabies virus (PRV), imaged inside intact virions at ~7-Å resolution. From these, we developed a complete model of subunit and domain organization and identified extensive networks of subunit contacts that underpin capsid stability and form a pathway that may signal the completion of DNA packaging from the capsid interior to outer surface, thereby initiating nuclear egress. Differences in the folding and orientation of subunit domains between herpesvirus capsids suggest that common elements have been modified for specific functions.
History
DepositionJul 17, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseApr 20, 2016-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 8000
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_6387.map.gz / Format: CCP4 / Size: 782.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationReconstruction of pseudorabies virus capsid imaged inside virions
Voxel sizeX=Y=Z: 2.16 Å
Density
Contour LevelBy AUTHOR: 8000.0 / Movie #1: 8000
Minimum - Maximum-17559.0 - 32443.0
Average (Standard dev.)1084.363403320000089 (±3472.1518554700001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions749749749
Spacing749749749
CellA=B=C: 1617.8401 Å
α=β=γ: 90.000084 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.162.162.16
M x/y/z749749749
origin x/y/z0.0000.0000.000
length x/y/z1617.8401617.8401617.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS749749749
D min/max/mean-17559.00032443.0001084.363

-
Supplemental data

-
Sample components

-
Entire : Capsid of pseudorabies virus imaged in intact virions

EntireName: Capsid of pseudorabies virus imaged in intact virions
Components
  • Sample: Capsid of pseudorabies virus imaged in intact virions
  • Virus: Suid herpesvirus 1

-
Supramolecule #1000: Capsid of pseudorabies virus imaged in intact virions

SupramoleculeName: Capsid of pseudorabies virus imaged in intact virions / type: sample / ID: 1000 / Oligomeric state: Icosahedral T=16 / Number unique components: 1
Molecular weightExperimental: 200 MDa / Theoretical: 200 MDa

-
Supramolecule #1: Suid herpesvirus 1

SupramoleculeName: Suid herpesvirus 1 / type: virus / ID: 1 / Details: Native Becker / NCBI-ID: 10345 / Sci species name: Suid herpesvirus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Sus scrofa (pig) / synonym: VERTEBRATES
Host systemOrganism: Chlorocebus aethiops (grivet) / Recombinant cell: green monkey kidney (Vero) cells
Molecular weightExperimental: 200 MDa / Theoretical: 200 MDa
Virus shellShell ID: 1 / Diameter: 1250 Å / T number (triangulation number): 16

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

GridDetails: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: 6 second blot

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 75,000x magnification.
DetailsNanoprobe
DateApr 14, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 32956 / Average electron dose: 30 e/Å2 / Details: 2 second exposures; no use of movie mode
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: By micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: OTHER / Software - Name: AUTO3DEM, CTFFIND3
Details: Final map calculated from 25637 images of capsids inside virions. Resolution was verified by comparing cryoEM data with band-limited renditions of the HSV VP5 upper domain fragment, PDB 1NO7.
Number images used: 13242
DetailsManual selection, processing with AUTO3DEM

-
Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A
SoftwareName: Chimera
DetailsManual docking
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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