[English] 日本語
Yorodumi
- EMDB-1018: The first step: activation of the Semliki Forest virus spike prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1018
TitleThe first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike.
Map dataSemliki forest virus
Sample
  • Sample: Semliki forest mSQL
  • Virus: Semliki forest virus
Biological speciesSemliki forest virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsFuller SD
CitationJournal: J Mol Biol / Year: 1998
Title: The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike.
Authors: I Ferlenghi / B Gowen / F de Haas / E J Mancini / H Garoff / M Sjöberg / S D Fuller /
Abstract: The structure of the particle formed by the SFVmSQL mutant of Semliki Forest virus (SFV) has been defined by cryo-electron microscopy and image reconstruction to a resolution of 21 A. The SQL ...The structure of the particle formed by the SFVmSQL mutant of Semliki Forest virus (SFV) has been defined by cryo-electron microscopy and image reconstruction to a resolution of 21 A. The SQL mutation blocks the cleavage of p62, the precursor of the spike proteins E2 and E3, which normally occurs in the trans-Golgi. The uncleaved spike protein is insensitive to the low pH treatment that triggers membrane fusion during entry of the wild-type virus. The conformation of the spike in the SFVmSQL particle should correspond to that of the inactive precursor found in the early stages of the secretory pathway. Comparison of this "precursor" structure with that of the mature, wild-type, virus allows visualization of the changes that lead to activation, the first step in the pathway toward fusion. We find that the conformational change in the spike is dramatic but localized. The projecting domains of the spikes are completely separated in the precursor and close to generate a cavity in the mature spike. E1, the fusion peptide-bearing protein, interacts only with the p62 in its own third of the trimer before cleavage and then collapses to form a trimer of heterotrimers (E1E2E3)3 surrounding the cavity, poised for the pH-induced conformational change that leads to fusion. The capsid, transmembrane regions and the spike skirts (thin layers of protein that link spikes above the membrane) remain unchanged by cleavage. Similarly, the interactions of the spikes with the nucleocapsid through the transmembrane domains remain constant. Hence, the interactions that lead to virus assembly are unaffected by the SFVmSQL mutation.
History
DepositionDec 12, 2002-
Header (metadata) releaseJan 6, 2003-
Map releaseJan 6, 2003-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 961
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 961
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1018.gif

Downloads & links

-
Map

FileDownload / File: emd_1018.map.gz / Format: CCP4 / Size: 31.3 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationSemliki forest virus
Voxel sizeX=Y=Z: 1 Å
Density
Contour Level1: 992.0 / Movie #1: 961
Minimum - Maximum-6796.0 - 3204.0
Average (Standard dev.)7.4848 (±394.451000000000022)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-6796.0003204.0007.485

-
Supplemental data

-
Sample components

-
Entire : Semliki forest mSQL

EntireName: Semliki forest mSQL
Components
  • Sample: Semliki forest mSQL
  • Virus: Semliki forest virus

-
Supramolecule #1000: Semliki forest mSQL

SupramoleculeName: Semliki forest mSQL / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Semliki forest virus

SupramoleculeName: Semliki forest virus / type: virus / ID: 1 / Name.synonym: semliki forest m SQL / Details: mSQL mutation. / NCBI-ID: 11033 / Sci species name: Semliki forest virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: semliki forest m SQL
Host (natural)Organism: baby hamster kidney 21 cells (unknown) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: envelope / T number (triangulation number): 4
Virus shellShell ID: 2 / Name: nucleo capsid / T number (triangulation number): 4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.4 / Details: tris(10mM) NaCL (100mM) ph 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 37 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: EMBL plunger with warm humid air spray
Method: blot for 2 sec Graticule grids were used to maintain

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
TemperatureAverage: 105 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PERKIN ELMER / Digitization - Sampling interval: 20 µm / Average electron dose: 8 e/Å2 / Camera length: 44 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 7.628 µm / Nominal defocus min: 0.975 µm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: ctf multiplication and summation of normalized reconstructions
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMBL / Number images used: 62
Final angle assignmentDetails: sufficient to give maximum inverse eigen value of 0.1

+
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://pdbjlvh1.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