[English] 日本語
Yorodumi
- EMDB-32412: Cryo-EM structure of alphavirus, Getah virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32412
TitleCryo-EM structure of alphavirus, Getah virus
Map dataCryo-EM structure of Getah virus, Block-based reconstruction method.
Sample
  • Virus: Getah virus
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesGetah virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang M / Sun ZZ / Wang JF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Implications for the pathogenicity and antigenicity of alpha viruses revealed by a 3.5 angstrom Cryo-EM structure of Getah virus
Authors: Wang M / Sun ZZ / Wang JF
History
DepositionDec 18, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 2, 2022-
Current statusNov 2, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32412.png

Downloads & links

-
Map

FileDownload / File: emd_32412.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Getah virus, Block-based reconstruction method.
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.07085458 - 0.107337
Average (Standard dev.)6.2851934e-05 (±0.0044403933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-299-299-299
Dimensions600600600
Spacing600600600
CellA=B=C: 816.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Getah virus

EntireName: Getah virus
Components
  • Virus: Getah virus
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2

-
Supramolecule #1: Getah virus

SupramoleculeName: Getah virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 59300 / Sci species name: Getah virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Getah virus

-
Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Getah virus
Molecular weightTheoretical: 47.62077 KDa
SequenceString: YEHTATIPNV VGFPYKAHIE RNGFSPMTLQ LEVLGTSLEP TLNLEYITCE YKTVVPSPYI KCCGTSECRS MERPDYQCQV YTGVYPFMW GGAYCFCDTE NTQLSEAYVD RSDVCKHDHA AAYKAHTAAM KATIRISYGN LNQTTTAFVN GEHTVTVGGS R FTFGPIST ...String:
YEHTATIPNV VGFPYKAHIE RNGFSPMTLQ LEVLGTSLEP TLNLEYITCE YKTVVPSPYI KCCGTSECRS MERPDYQCQV YTGVYPFMW GGAYCFCDTE NTQLSEAYVD RSDVCKHDHA AAYKAHTAAM KATIRISYGN LNQTTTAFVN GEHTVTVGGS R FTFGPIST AWTPFDNKIV VYKNDVYNQD FPPYGSGQPG RFGDIQSRTV ESKDLYANTA LKLSRPSSGT VHVPYTQTPS SF KYWIKER GTSLNDKAPF GCVIKTNPVR AENCAVGNIP VSMDIPDTAF TRVIDAPAVT NLECQVAVCT HSSDFGGIAT LTF KTDKPG KCAVHSHSNV ATIQEAAVDI KTDGKITLHF STASASPAFK VSVCSAKTTC MAACEPPKDH IVPYGASHNN QVFP DMSGT AMTWVQRVAG GLGGLTLAAV AVLILVTCVT MRR

-
Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Getah virus
Molecular weightTheoretical: 46.416793 KDa
SequenceString: SVTEHFNVYK ATKPYLAYCA DCGDGQFCYS PVAIEKIRDE ASDGMIKIQV AAQIGINKGG THEHNKIRYI AGHDMKEANR DSLQVHTSG VCAIRGTMGH FIVAYCPPGD ELKVQFQDAE SHTQACKVQY KHAPAPVGRE KFTVRPHFGI EVPCTTYQLT T APTEEEID ...String:
SVTEHFNVYK ATKPYLAYCA DCGDGQFCYS PVAIEKIRDE ASDGMIKIQV AAQIGINKGG THEHNKIRYI AGHDMKEANR DSLQVHTSG VCAIRGTMGH FIVAYCPPGD ELKVQFQDAE SHTQACKVQY KHAPAPVGRE KFTVRPHFGI EVPCTTYQLT T APTEEEID MHTPPDIPDI TLLSQQSGNV KITAGGKTIR YNCTCGSGNV GTTSSDKTIN SCKIAQCHAA VTNHDKWQYT SS FVPRADQ LSRKGKVHVP FPLTNSTCRV PVARAPGVTY GKRELTVKLH PDHPTLLTYR SLGADPRPYE EWIDRYVERT IPV TEEGIE YRWGNNPPVR LWAQLTTEGK PHGWPHEIIL YYYGLYPAAT IAAVSAAGLA VVLSLLASCY MFATARRKCL TPYA LTPGA VVPVTLGVLC CAPRAHA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

-
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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 36066 / Details: region for particle picking
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30996

+
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