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- EMDB-6706: Prefusion structure of MERS-CoV spike glycoprotein, conformation 1 -

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Basic information

Entry
Database: EMDB / ID: 6706
TitlePrefusion structure of MERS-CoV spike glycoprotein, conformation 1
Map data
SampleMERS-CoV spike trimer:
S protein
Function / homologyCoronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain superfamily / Coronavirus S2 glycoprotein / Spike receptor binding domain / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated virion attachment to host cell / fusion of virus membrane with host endosome membrane ...Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain / Coronavirus S2 glycoprotein / Spike receptor binding domain superfamily / Coronavirus S2 glycoprotein / Spike receptor binding domain / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated virion attachment to host cell / fusion of virus membrane with host endosome membrane / viral envelope / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane / Spike glycoprotein / S protein
Function and homology information
SourceMiddle East respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsYuan Y / Cao D / Zhang Y / Ma J / Qi J / Wang Q / Lu G / Wu Y / Yan J / Shi Y / Zhang X / Gao GF
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
Validation ReportPDB-ID: 5x5c

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: 0.0618
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0618
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5x5c
  • Surface level: 0.0618
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6706.map.gz (map file in CCP4 format, 23329 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.3 Å/pix.
= 234. Å
180 pix
1.3 Å/pix.
= 234. Å
180 pix
1.3 Å/pix.
= 234. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.0618 (by author), 0.0618 (movie #1):
Minimum - Maximum-0.11593462 - 0.21254966
Average (Standard dev.)0.00003375553 (0.012735819)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin-90.0-90.0-90.0
Limit89.089.089.0
Spacing180180180
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z234.000234.000234.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-0.1160.2130.000

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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: 2

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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
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, S protein

ProteinName: S protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 145.856203 kDa
SourceSpecies: Middle East respiratory syndrome coronavirus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
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 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 60000
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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