[English] 日本語
Yorodumi
- EMDB-32426: Cryo-EM structure of alphavirus, Getah virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32426
TitleCryo-EM structure of alphavirus, Getah virus
Map dataCryo-EM structure of Getah capsid protein, Block-based reconstruction (Block 1).
Sample
  • Virus: Getah virus
    • Protein or peptide: Spike glycoprotein E1
    • Protein or peptide: Spike glycoprotein E2
    • Protein or peptide: Capsid protein
Keywordsalphavirus / Getah virus / Togaviridae / structural genomics / VIRAL PROTEIN
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 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / 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: 3.8 Å
AuthorsWang M / Sun ZZ
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 20, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32426.png

Downloads & links

-
Map

FileDownload / File: emd_32426.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Getah capsid protein, Block-based reconstruction (Block 1).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0725077 - 0.11874988
Average (Standard dev.)0.00006467506 (±0.0044640405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 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
    • Protein or peptide: Capsid protein

-
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: SUBSPECIES / Virus enveloped: Yes / Virus empty: No

-
Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

UniProtKB: Structural polyprotein

-
Macromolecule #2: Spike glycoprotein E2

MacromoleculeName: Spike glycoprotein E2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

UniProtKB: Structural polyprotein

-
Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Getah virus
Molecular weightTheoretical: 30.200117 KDa
SequenceString: MNYIPTQTFY GRRWRPRPAY RPWRVPMQPA PPMVIPELQT PIVQAQQMQQ LISAVSALTT KQNGKAPKKP KKKPQKAKAK KNEQQKKNE NKKPPPKQKN PAKKKKPGKR ERMCMKIEND CIFEVKLDGK VTGYACLVGD KVMKPAHVKG VIDNPDLAKL T YKKSSKYD ...String:
MNYIPTQTFY GRRWRPRPAY RPWRVPMQPA PPMVIPELQT PIVQAQQMQQ LISAVSALTT KQNGKAPKKP KKKPQKAKAK KNEQQKKNE NKKPPPKQKN PAKKKKPGKR ERMCMKIEND CIFEVKLDGK VTGYACLVGD KVMKPAHVKG VIDNPDLAKL T YKKSSKYD LECAQIPVHM KSDASKYTHE KPEGHYNWHH GAVQYSGGRF TIPTGAGKPG DSGRPIFDNK GRVVAIVLGG AN EGARTAL SVVTWTKDMV TRYTPEGTEE W

UniProtKB: Structural polyprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30996
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
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