[English] 日本語
Yorodumi
- EMDB-8734: Electron cryo-microscopy of "immature" Chikungunya VLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8734
TitleElectron cryo-microscopy of "immature" Chikungunya VLP
Map dataChikungunya virus strain Senegal 37997
Sample
  • Virus: Chikungunya virus strain Senegal 37997
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E3 envelope glycoprotein
    • Protein or peptide: capsid proteinCapsid
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein
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 / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm
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
Togavirin / Togavirin / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus strain Senegal 37997 / Chikungunya virus (strain 37997)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsRossmann MG / Yap ML
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095366 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural studies of Chikungunya virus maturation.
Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann /
Abstract: Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. ...Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-Å resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus.
History
DepositionMay 18, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseDec 6, 2017-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5vu2
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5vu2
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8734.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChikungunya virus strain Senegal 37997
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 1 / Movie #1: 1
Minimum - Maximum-5 - 5
Average (Standard dev.)0.029038956 (±0.4375374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-384-384-384
Dimensions768768768
Spacing768768768
CellA=B=C: 998.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z768768768
origin x/y/z0.0000.0000.000
length x/y/z998.400998.400998.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-384-384-384
NC/NR/NS768768768
D min/max/mean-5.0005.0000.029

-
Supplemental data

-
Sample components

-
Entire : Chikungunya virus strain Senegal 37997

EntireName: Chikungunya virus strain Senegal 37997
Components
  • Virus: Chikungunya virus strain Senegal 37997
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E3 envelope glycoprotein
    • Protein or peptide: capsid proteinCapsid
    • Protein or peptide: E1 envelope glycoprotein
    • Protein or peptide: E2 envelope glycoprotein

-
Supramolecule #1: Chikungunya virus strain Senegal 37997

SupramoleculeName: Chikungunya virus strain Senegal 37997 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 371095 / Sci species name: Chikungunya virus strain Senegal 37997 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: Human embryonic kidney / Recombinant plasmid: pUC119

-
Macromolecule #1: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 95.538164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STKDNFNVYK ATRPYLAHCP DCGEGHSCHS PVALERIRNE ATDGTLKIQV SLQIGIKTDD SHDWTKLRYM DNHMPADAER AGLFVRTSA PCTITGTMGH FILARCPKGE TLTVGFTDSR KISHSCTHPF HHDPPVIGRE KFHSRPQHGK ELPCSTYVQS T AATTEEIE ...String:
STKDNFNVYK ATRPYLAHCP DCGEGHSCHS PVALERIRNE ATDGTLKIQV SLQIGIKTDD SHDWTKLRYM DNHMPADAER AGLFVRTSA PCTITGTMGH FILARCPKGE TLTVGFTDSR KISHSCTHPF HHDPPVIGRE KFHSRPQHGK ELPCSTYVQS T AATTEEIE VHMPPDTPDR TLMSQQSGNV KITVNGQTVR YKCNCGGSNE GLTTTDKVIN NCKVDQCHAA VTNHKKWQYN SP LVPRNAE LGDRKGKIHI PFPLANVTCR VPKARNPTVT YGKNQVIMLL YPDHPTLLSY RNMGEEPNYQ EEWVMHKKEV VLT VPTEGL EVTWGNNEPY KYWPQLSTNG TAHGHPHEII LYYYELYPTM TVVVVSVATF ILLSMVGMAA GMCMCARRRC ITPY ELTPG ATVPFLLSLI CCIRTAKAAT YQEAAIYLWN EQQPLFWLQA LIPLAALIVL CNCLRLLPCC CKTLAFLAVM SVGAH TVSA YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KNLPDY SCK VFTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVTAYAN GDHAVTV KD AKFIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQA P SGFKYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNMP ISIDIPEAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVA IIKYAASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHP

-
Macromolecule #2: E3 envelope glycoprotein

MacromoleculeName: E3 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 6.92699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PVMCLLANTT FPCSQPPCTP CCYEKEPEET LRMLEDNVMR PGYYQLLQAS LTCSPHRQRE

-
Macromolecule #3: capsid protein

MacromoleculeName: capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus (strain 37997) / Strain: 37997
Molecular weightTheoretical: 16.229508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CIFEVKHEGK VMGYACLVGD KVMKPAHVKG TIDNADLAKL AFKRSSKYDL ECAQIPVHMK SDASKFTHEK PEGYYNWHHG AVQYSGGRF TIPTGAGKPG DSGRPIFDNK GRVVAIVLGG ANEGARTALS VVTWNKDIVT KITPEGAEEW

-
Macromolecule #4: E1 envelope glycoprotein

MacromoleculeName: E1 envelope glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 4.810723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
HTTLGVQDIS TTAMSWVQKI TGGVGLIVAV AALILIVVLC VSFSRH

-
Macromolecule #5: E2 envelope glycoprotein

MacromoleculeName: E2 envelope glycoprotein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997
Molecular weightTheoretical: 8.817458 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
STNGTAHGHP HEIILYYYEL YPTMTVVIVS VASFVLLSMV GTAVGMCVCA RRRCITPYEL TPGATVPFLL SLLCCVRTTK A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 72944
FSC plot (resolution estimation)

+
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