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- EMDB-6704: Prefusion structure of MERS-CoV spike glycoprotein, three-fold sy... -

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Basic information

Entry
Database: EMDB / ID: 6704
TitlePrefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry
Map data
SampleMERS-CoV spike trimer
Function/homologyhost cell endoplasmic reticulum-Golgi intermediate compartment membrane / Spike receptor binding domain / Spike receptor binding domain superfamily / Coronovirus spike glycoprotein, heptad repeat 2 domain / Coronavirus S2 glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain / membrane fusion / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Spike receptor binding domain / Spike receptor binding domain superfamily / Coronovirus spike glycoprotein, heptad repeat 2 domain / Coronavirus S2 glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain / membrane fusion / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / pathogenesis / viral envelope / virion membrane / integral component of membrane / Spike glycoprotein / S protein
Function and homology information
SourceMiddle East respiratory syndrome coronavirus / virus /
Methodsingle particle reconstruction, at 3.7 Å resolution
AuthorsYuan Y / Cao D
CitationJournal: Nat Commun / Year: 2017
Title: Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains.
Authors: Yuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao
Abstract: The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and ...The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.
Validation ReportPDB-ID: 5x59

SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: May 24, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0615
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0615
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5x59
  • Surface level: 0.0615
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_6704.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.0615 (by author), 0.0615 (movie #1):
Minimum - Maximum-0.23481733 - 0.4019932
Average (Standard dev.)3.0789917E-5 (0.011461312)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin-128-128-128
Limit127127127
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.2350.4020.000

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Supplemental data

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Sample components

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Entire MERS-CoV spike trimer

EntireName: MERS-CoV spike trimer / Number of components: 3

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Component #1: protein, MERS-CoV spike trimer

ProteinName: MERS-CoV spike trimer / Recombinant expression: No
SourceSpecies: Middle East respiratory syndrome coronavirus / virus /
Source (engineered)Expression System: Spodoptera frugiperda / arthropod / Fall armyworm

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Component #2: protein, S protein

ProteinName: S protein / Recombinant expression: No
MassTheoretical: 145.856203 kDa
Source (engineered)Expression System: Middle East respiratory syndrome coronavirus / virus /

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINE / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 60000
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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