[English] 日本語
Yorodumi
- EMDB-7040: Tectonic conformational changes of a coronavirus spike glycoprote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7040
TitleTectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
Map dataTectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
Sample
  • Complex: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
    • Protein or peptide: Spike glycoproteinSpike protein
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell Golgi apparatus / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / identical protein binding
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesMurine hepatitis virus / Murine coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWalls AC / Tortorici MA / Snijder J / Xiong X / Bosch BJ / Rey FA / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM120553 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion.
Authors: Alexandra C Walls / M Alejandra Tortorici / Joost Snijder / Xiaoli Xiong / Berend-Jan Bosch / Felix A Rey / David Veesler /
Abstract: The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. The coronavirus spike (S) glycoprotein initiates ...The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. The coronavirus spike (S) glycoprotein initiates infection by promoting fusion of the viral and cellular membranes through conformational changes that remain largely uncharacterized. Here we report the cryoEM structure of a coronavirus S glycoprotein in the postfusion state, showing large-scale secondary, tertiary, and quaternary rearrangements compared with the prefusion trimer and rationalizing the free-energy landscape of this conformational machine. We also biochemically characterized the molecular events associated with refolding of the metastable prefusion S glycoprotein to the postfusion conformation using limited proteolysis, mass spectrometry, and single-particle EM. The observed similarity between postfusion coronavirus S and paramyxovirus F structures demonstrates that a conserved refolding trajectory mediates entry of these viruses and supports the evolutionary relatedness of their fusion subunits. Finally, our data provide a structural framework for understanding the mode of neutralization of antibodies targeting the fusion machinery and for engineering next-generation subunit vaccines or inhibitors against this medically important virus family.
History
DepositionSep 22, 2017-
Header (metadata) releaseOct 4, 2017-
Map releaseOct 4, 2017-
UpdateJan 1, 2020-
Current statusJan 1, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6b3o
  • Surface level: 0.16
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7040.png

Downloads & links

-
Map

FileDownload / File: emd_7040.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.16
Minimum - Maximum-0.5127941 - 0.7845471
Average (Standard dev.)0.00019818555 (±0.008341526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z435.200435.200435.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.5130.7850.000

-
Supplemental data

-
Sample components

-
Entire : Mouse hepatitis virus spike glycoprotein (S2 subunit) in the post...

EntireName: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
Components
  • Complex: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
    • Protein or peptide: Spike glycoproteinSpike protein

-
Supramolecule #1: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the post...

SupramoleculeName: Mouse hepatitis virus spike glycoprotein (S2 subunit) in the postfusion conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Murine hepatitis virus
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 180 KDa

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine coronavirus / Strain: A59
Molecular weightTheoretical: 66.199094 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MKLCILLAVV AFVGLSLGRS LASVSTGYRL TTFEPYTPML VNDSVQSVDG LYEMQIPTNF TIGHHEEFIQ TRSPKVTIDC AAFVCGDNT ACRQQLVEYG SFCVNVNAIL NEVNNLLDNM QLQVASALMQ GVTISSRLPD GISGPIDDIN FSPLLGCIGS T CAEDGNGP ...String:
MKLCILLAVV AFVGLSLGRS LASVSTGYRL TTFEPYTPML VNDSVQSVDG LYEMQIPTNF TIGHHEEFIQ TRSPKVTIDC AAFVCGDNT ACRQQLVEYG SFCVNVNAIL NEVNNLLDNM QLQVASALMQ GVTISSRLPD GISGPIDDIN FSPLLGCIGS T CAEDGNGP SAIRGRSAIE DLLFDKVKLS DVGFVEAYNN CTGGQEVRDL LCVQSFNGIK VLPPVLSESQ ISGYTTGATA AA MFPPWSA AAGVPFSLSV QYRINGLGVT MNVLSENQKM IASAFNNALG AIQDGFDATN SALGKIQSVV NANAEALNNL LNQ LSNRFG AISASLQEIL TRLEAVEAKA QIDRLINGRL TALNAYISKQ LSDSTLIKVS AAQAIEKVNE CVKSQTTRIN FCGN GNHIL SLVQNAPYGL YFIHFSYVPI SFTTANVSPG LCISGDRGLA PKAGYFVQDD GEWKFTGSSY YYPEPITDKN SVIMS SCAV NYTKAPEVFL NTSIPNPPDF KEELDKWFKN QTSIAPDLSL DFEKLNVTLL DLTYEMNRIQ DAIKKLNESY INLIKR MKQ IEDKIEEIES KQKKIENEIA RIKKIKLVPR GSLEWSHPQF EK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

-
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: RELION (ver. 2.0.3)
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0.3)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.3) / Number images used: 106000

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6b3o:
Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

+
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