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- EMDB-7608: SARS spike glycoprotein, focused refinement of S1 CTD bound to ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-7608
TitleSARS spike glycoprotein, focused refinement of S1 CTD bound to ACE2
Map data
SampleSARS Spike Glycoprotein complexed to ACE2 receptor
  • SARS spike glycoprotein
  • Angiotensin converting enzyme 2Angiotensin-converting enzyme
Function / homology
Function and homology information


positive regulation of L-proline import across plasma membrane / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / positive regulation of cardiac muscle contraction / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity ...positive regulation of L-proline import across plasma membrane / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / tryptophan transport / positive regulation of cardiac muscle contraction / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / peptidyl-dipeptidase activity / regulation of vasoconstriction / blood vessel diameter maintenance / angiotensin maturation / carboxypeptidase activity / brush border membrane / metallocarboxypeptidase activity / regulation of cytokine production / negative regulation of signaling receptor activity / regulation of cardiac conduction / regulation of transmembrane transporter activity / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / metallopeptidase activity / virus receptor activity / positive regulation of reactive oxygen species metabolic process / host cell surface receptor binding / endocytosis involved in viral entry into host cell / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / apical plasma membrane / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / membrane raft / go:0009405: / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / integral component of membrane / extracellular region / identical protein binding / plasma membrane / cytoplasm
Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Collectrin domain / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Fibritin C-terminal / Spike glycoprotein S2, coronavirus / Peptidase M2, peptidyl-dipeptidase A / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus
Fibritin / Spike glycoprotein / Angiotensin-converting enzyme 2
Biological speciesSARS coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
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 /
Abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 as a highly transmissible pathogenic human betacoronavirus. The viral spike glycoprotein (S) utilizes angiotensin-converting ...Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2002 as a highly transmissible pathogenic human betacoronavirus. The viral spike glycoprotein (S) utilizes angiotensin-converting enzyme 2 (ACE2) as a host protein receptor and mediates fusion of the viral and host membranes, making S essential to viral entry into host cells and host species tropism. As SARS-CoV enters host cells, the viral S is believed to undergo a number of conformational transitions as it is cleaved by host proteases and binds to host receptors. We recently developed stabilizing mutations for coronavirus spikes that prevent the transition from the pre-fusion to post-fusion states. Here, we present cryo-EM analyses of a stabilized trimeric SARS-CoV S, as well as the trypsin-cleaved, stabilized S, and its interactions with ACE2. Neither binding to ACE2 nor cleavage by trypsin at the S1/S2 cleavage site impart large conformational changes within stabilized SARS-CoV S or expose the secondary cleavage site, S2'.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMar 21, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 11, 2018-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_7608.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 360 pix.
= 370.8 Å
1.03 Å/pix.
x 360 pix.
= 370.8 Å
1.03 Å/pix.
x 360 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 LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.04818823 - 0.08661161
Average (Standard dev.)-0.00032229055 (±0.0023938906)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 370.8 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0480.087-0.000

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Supplemental data

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Segmentation: #1

Fileemd_7608_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: SARS Spike Glycoprotein, Stabilized variant, single upwards S1...

Fileemd_7608_half_map_1.map
AnnotationSARS Spike Glycoprotein, Stabilized variant, single upwards S1 CTD conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: SARS Spike Glycoprotein, Stabilized variant, single upwards S1...

Fileemd_7608_half_map_2.map
AnnotationSARS Spike Glycoprotein, Stabilized variant, single upwards S1 CTD conformation
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: 52916
3D reconstructionSoftware: RELION / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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