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- EMDB-7601: SARS spike glycoprotein, stabilized variant, S1 CTD configuration... -

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Entry
Database: EMDB / ID: 7601
TitleSARS spike glycoprotein, stabilized variant, S1 CTD configuration: ACE2-bound, downwards, upwards
Map dataSARS Spike Glycoprotein, Stabilized variant, single upwards S1 CTD conformation
SampleSARS Spike Glycoprotein complexed to ACE2 receptor
  • SARS spike glycoprotein
  • Angiotensin converting enzyme 2Angiotensin-converting enzyme
Function / homologySpike glycoprotein, N-terminal / Renal amino acid transporter / Angiotensin-converting enzyme / Coronavirus S2 glycoprotein / Fibritin C-terminal region / Collectrin domain / Spike receptor binding domain / Spike glycoprotein N-terminal domain / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike receptor binding domain superfamily ...Spike glycoprotein, N-terminal / Renal amino acid transporter / Angiotensin-converting enzyme / Coronavirus S2 glycoprotein / Fibritin C-terminal region / Collectrin domain / Spike receptor binding domain / Spike glycoprotein N-terminal domain / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike receptor binding domain superfamily / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain / Metabolism of Angiotensinogen to Angiotensins / Fibritin C-terminal / Coronavirus S2 glycoprotein / Peptidase M2, peptidyl-dipeptidase A / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / tryptophan transport / positive regulation of cardiac muscle contraction / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / receptor biosynthetic process / regulation of systemic arterial blood pressure by renin-angiotensin / exopeptidase activity / regulation of blood vessel diameter / regulation of vasoconstriction / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / carboxypeptidase activity / angiotensin maturation / brush border membrane / receptor-mediated virion attachment to host cell / regulation of cytokine production / regulation of cardiac conduction / metallocarboxypeptidase activity / host cell surface receptor binding / virus receptor activity / positive regulation of reactive oxygen species metabolic process / regulation of inflammatory response / regulation of cell population proliferation / fusion of virus membrane with host endosome membrane / viral entry into host cell / endopeptidase activity / viral envelope / pathogenesis / membrane raft / host cell plasma membrane / virion membrane / cell surface / zinc ion binding / extracellular exosome / extracellular space / integral component of membrane / extracellular region / identical protein binding / plasma membrane / cytoplasm / Fibritin / Spike glycoprotein / Angiotensin-converting enzyme 2
Function and homology information
SourceSARS coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 7.6 Å resolution
AuthorsKirchdoerfer RN / Wang N / Pallesen J / Turner HL / Cottrell CA / McLellan JS / Ward AB
CitationJournal: Sci Rep / Year: 2018
Title: Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis.
Authors: Robert N Kirchdoerfer / Nianshuang Wang / Jesper Pallesen / Daniel Wrapp / Hannah L Turner / Christopher A Cottrell / Kizzmekia S Corbett / Barney S Graham / Jason S McLellan / Andrew B Ward
DateDeposition: Mar 21, 2018 / Header (metadata) release: Apr 11, 2018 / Map release: Apr 11, 2018 / Last update: Dec 12, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7601.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.03 Å/pix.
= 370.8 Å
360 pix
1.03 Å/pix.
= 370.8 Å
360 pix
1.03 Å/pix.
= 370.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.012128318 - 0.041741647
Average (Standard dev.)0.00032188412 (0.0022893446)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 370.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z370.800370.800370.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-153-266-98
NX/NY/NZ528514389
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0120.0420.000

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Supplemental data

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Mask #1

Fileemd_7601_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire SARS Spike Glycoprotein complexed to ACE2 receptor

EntireName: SARS Spike Glycoprotein complexed to ACE2 receptor / Number of components: 3

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Component #1: protein, SARS Spike Glycoprotein complexed to ACE2 receptor

ProteinName: SARS Spike Glycoprotein complexed to ACE2 receptor / Recombinant expression: No
MassTheoretical: 620 kDa
SourceSpecies: SARS coronavirus / Strain: Tor2
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293F

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Component #2: protein, SARS spike glycoprotein

ProteinName: SARS spike glycoprotein / Recombinant expression: No
SourceSpecies: SARS coronavirus / Strain: Tor2
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Angiotensin converting enzyme 2

ProteinName: Angiotensin converting enzyme 2Angiotensin-converting enzyme
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.35 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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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: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 6755
3D reconstructionSoftware: RELION / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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