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- EMDB-6526: Cryo-electron microscopy structure of a coronavirus spike glycopr... -

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Basic information

Entry
Database: EMDB / ID: EMD-6526
TitleCryo-electron microscopy structure of a coronavirus spike glycoprotein trimer
Map dataReconstruction of a furin cleavage site mutant
Sample
  • Sample: Murine hepatitis virus protein S
  • Protein or peptide: Murine hepatitis virus protein S
KeywordsCoronavirus / viral fusion proteins / viral spike / peplomer
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
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWalls AC / Tortorici MA / Bosch BJ / Frenz BJ / Rottier PJM / DiMaio F / Rey FA / Veesler D
CitationJournal: Nature / Year: 2016
Title: Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer.
Authors: Alexandra C Walls / M Alejandra Tortorici / Berend-Jan Bosch / Brandon Frenz / Peter J M Rottier / Frank DiMaio / Félix 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. Entry of coronaviruses into cells is mediated by the ...The tremendous pandemic potential of coronaviruses was demonstrated twice in the past few decades by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. S also contains the principal antigenic determinants and is the target of neutralizing antibodies. Here we present the structure of a mouse coronavirus S trimer ectodomain determined at 4.0 Å resolution by single particle cryo-electron microscopy. It reveals the metastable pre-fusion architecture of S and highlights key interactions stabilizing it. The structure shares a common core with paramyxovirus F proteins, implicating mechanistic similarities and an evolutionary connection between these viral fusion proteins. The accessibility of the highly conserved fusion peptide at the periphery of the trimer indicates potential vaccinology strategies to elicit broadly neutralizing antibodies against coronaviruses. Finally, comparison with crystal structures of human coronavirus S domains allows rationalization of the molecular basis for species specificity based on the use of spatially contiguous but distinct domains.
History
DepositionNov 19, 2015-
Header (metadata) releaseFeb 3, 2016-
Map releaseFeb 3, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jcl
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jcl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6526.gif

Downloads & links

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Map

FileDownload / File: emd_6526.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a furin cleavage site mutant
Voxel sizeX=Y=Z: 1.46 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.31347367 - 0.45625103
Average (Standard dev.)0.00024176 (±0.00649352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 420.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.461.461.46
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z420.480420.480420.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3130.4560.000

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Supplemental data

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Sample components

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Entire : Murine hepatitis virus protein S

EntireName: Murine hepatitis virus protein S
Components
  • Sample: Murine hepatitis virus protein S
  • Protein or peptide: Murine hepatitis virus protein S

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Supramolecule #1000: Murine hepatitis virus protein S

SupramoleculeName: Murine hepatitis virus protein S / type: sample / ID: 1000 / Oligomeric state: Trimer / Number unique components: 1
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: Murine hepatitis virus protein S

MacromoleculeName: Murine hepatitis virus protein S / type: protein_or_peptide / ID: 1 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Murine hepatitis virus / Strain: A59 / synonym: MHV
Molecular weightTheoretical: 140 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: S2
SequenceUniProtKB: Spike glycoprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.85 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris-HCl, 100 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 3.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38022 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateDec 9, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1600 / Average electron dose: 53 e/Å2
Details: Every image is the average of 38 frames recorded by the direct electron detector.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 82000

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Atomic model buiding 1

Initial modelPDB ID:

4kqz

SoftwareName: Rosetta, Coot, Chimera
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3jcl:
Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

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Atomic model buiding 2

Initial modelPDB ID:

4h14

SoftwareName: Rosetta, Coot, Chimera
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3jcl:
Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

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Atomic model buiding 3

Initial modelPDB ID:

3r4d

SoftwareName: Rosetta, Coot, Chimera
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3jcl:
Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

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