[English] 日本語
Yorodumi
- EMDB-1118: Structural polymorphism of the major capsid protein of a double-s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1118
TitleStructural polymorphism of the major capsid protein of a double-stranded RNA virus: an amphipathic alpha helix as a molecular switch.
Map dataThree-dimensional density map of IBDV chimeric capsids at 15 A resolution, viewed along 2 fold axis of symmetry. The chimeric IBDV protein is VP2, including 466 amino acid residues,with an N-terminal His tag
Sample
  • Sample: chimeric Infectious Bursal Disease Virus capsid
  • Virus: Infectious bursal disease virus (Gumboro virus)
Biological speciesInfectious bursal disease virus (Gumboro virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsSaugar I / Luque D / Ona A / Rodriguez JF / Carrascosa JL / Trus BL / Caston JR
CitationJournal: Structure / Year: 2005
Title: Structural polymorphism of the major capsid protein of a double-stranded RNA virus: an amphipathic alpha helix as a molecular switch.
Authors: Irene Saugar / Daniel Luque / Ana Oña / José F Rodríguez / José L Carrascosa / Benes L Trus / José R Castón /
Abstract: The infectious bursal disease virus T=13 viral particle is composed of two major proteins, VP2 and VP3. Here, we show that the molecular basis of the conformational flexibility of the major capsid ...The infectious bursal disease virus T=13 viral particle is composed of two major proteins, VP2 and VP3. Here, we show that the molecular basis of the conformational flexibility of the major capsid protein precursor, pVP2, is an amphipatic alpha helix formed by the sequence GFKDIIRAIR. VP2 containing this alpha helix is able to assemble into the T=13 capsid only when expressed as a chimeric protein with an N-terminal His tag. An amphiphilic alpha helix, which acts as a conformational switch, is thus responsible for the inherent structural polymorphism of VP2. The His tag mimics the VP3 C-terminal region closely and acts as a molecular triggering factor. Using cryo-electron microscopy difference imaging, both polypeptide elements were detected on the capsid inner surface. We propose that electrostatic interactions between these two morphogenic elements are transmitted to VP2 to acquire the competent conformations for capsid assembly.
History
DepositionMar 31, 2005-
Header (metadata) releaseMar 31, 2005-
Map releaseMay 11, 2006-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1118.gif

Downloads & links

-
Map

FileDownload / File: emd_1118.map.gz / Format: CCP4 / Size: 25.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree-dimensional density map of IBDV chimeric capsids at 15 A resolution, viewed along 2 fold axis of symmetry. The chimeric IBDV protein is VP2, including 466 amino acid residues,with an N-terminal His tag
Voxel sizeX=Y=Z: 4.2 Å
Density
Contour LevelBy AUTHOR: 30.5 / Movie #1: 35
Minimum - Maximum-109.0 - 189.0
Average (Standard dev.)14.99649715 (±45.47627258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-94-94-94
Dimensions189189189
Spacing189189189
CellA=B=C: 793.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z189189189
origin x/y/z0.0000.0000.000
length x/y/z793.800793.800793.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-80-80-80
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS-94-94-94
NC/NR/NS189189189
D min/max/mean-109.000189.00014.996

-
Supplemental data

-
Sample components

-
Entire : chimeric Infectious Bursal Disease Virus capsid

EntireName: chimeric Infectious Bursal Disease Virus capsid
Components
  • Sample: chimeric Infectious Bursal Disease Virus capsid
  • Virus: Infectious bursal disease virus (Gumboro virus)

-
Supramolecule #1000: chimeric Infectious Bursal Disease Virus capsid

SupramoleculeName: chimeric Infectious Bursal Disease Virus capsid / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Infectious bursal disease virus

SupramoleculeName: Infectious bursal disease virus / type: virus / ID: 1 / Name.synonym: HT-VP2-466 / NCBI-ID: 10995 / Sci species name: Infectious bursal disease virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: HT-VP2-466
Host (natural)Organism: Gallus gallus (chicken) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: HT-VP2-466 single layered capsid / Diameter: 700 Å / T number (triangulation number): 13

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 6.2 / Details: PIPES 25 mM, 150 mM NaCl, 20 mM CaCl2
GridDetails: Holey carbon film on copper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 111 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual / Method: double blotting

-
Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49700 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times
DetailsTEM Tecnai G2
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 82 / Average electron dose: 9 e/Å2 / Details: original images were binned 3X / Od range: 1 / Bits/pixel: 8

-
Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: emPFT / Number images used: 1557

+
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