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- EMDB-30305: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-30305
TitleCryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Map data
SampleCryo-EM structure of cat ACE2 and SARS-CoV-2 RBD:
cat ACE2 / SARS-CoV-2 RBD / Angiotensin-converting enzyme 2 / Spike protein S1 / ligand
Function / homology
Function and homology information


angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / carboxypeptidase activity / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / metallopeptidase activity / viral translation / virus receptor activity ...angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / carboxypeptidase activity / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / metallopeptidase activity / viral translation / virus receptor activity / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / viral protein processing / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / go:0009405: / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / cell surface / extracellular space / integral component of membrane / identical protein binding / plasma membrane / metal ion binding / cytoplasm
Spike glycoprotein, betacoronavirus / Spike glycoprotein S2 superfamily, coronavirus / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Collectrin domain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein S2, coronavirus ...Spike glycoprotein, betacoronavirus / Spike glycoprotein S2 superfamily, coronavirus / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Collectrin domain / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein S2, coronavirus / Peptidase M2, peptidyl-dipeptidase A / Coronavirus spike glycoprotein S1, C-terminal
Spike glycoprotein / Angiotensin-converting enzyme 2
Biological speciesFelis catus (domestic cat) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / Resolution: 3 Å
AuthorsGao GF / Wang QH / Wu L
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Cell Discov / Year: 2020
Title: Broad host range of SARS-CoV-2 and the molecular basis for SARS-CoV-2 binding to cat ACE2.
Authors: Lili Wu / Qian Chen / Kefang Liu / Jia Wang / Pengcheng Han / Yanfang Zhang / Yu Hu / Yumin Meng / Xiaoqian Pan / Chengpeng Qiao / Siyu Tian / Pei Du / Hao Song / Weifeng Shi / Jianxun Qi / ...Authors: Lili Wu / Qian Chen / Kefang Liu / Jia Wang / Pengcheng Han / Yanfang Zhang / Yu Hu / Yumin Meng / Xiaoqian Pan / Chengpeng Qiao / Siyu Tian / Pei Du / Hao Song / Weifeng Shi / Jianxun Qi / Hong-Wei Wang / Jinghua Yan / George Fu Gao / Qihui Wang /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the recent pandemic COVID-19, is reported to have originated from bats, with its intermediate host unknown to date. ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the recent pandemic COVID-19, is reported to have originated from bats, with its intermediate host unknown to date. Here, we screened 26 animal counterparts of the human ACE2 (hACE2), the receptor for SARS-CoV-2 and SARS-CoV, and found that the ACE2s from various species, including pets, domestic animals and multiple wild animals, could bind to SARS-CoV-2 receptor binding domain (RBD) and facilitate the transduction of SARS-CoV-2 pseudovirus. Comparing to SARS-CoV-2, SARS-CoV seems to have a slightly wider range in choosing its receptor. We further resolved the cryo-electron microscopy (cryo-EM) structure of the cat ACE2 (cACE2) in complex with the SARS-CoV-2 RBD at a resolution of 3 Å, revealing similar binding mode as hACE2 to the SARS-CoV-2 RBD. These results shed light on pursuing the intermediate host of SARS-CoV-2 and highlight the necessity of monitoring susceptible hosts to prevent further outbreaks.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 29, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c8d
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30305.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 180 pix.
= 178.875 Å
0.99 Å/pix.
x 180 pix.
= 178.875 Å
0.99 Å/pix.
x 180 pix.
= 178.875 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99375 Å
Density
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.08658028 - 0.15357167
Average (Standard dev.)0.00023852462 (±0.0047762245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 178.875 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.993750.993750.99375
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z178.875178.875178.875
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0870.1540.000

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Supplemental data

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Sample components

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Entire Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD

EntireName: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD / Number of components: 6

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Component #1: protein, Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD

ProteinName: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD / Recombinant expression: No
SourceSpecies: Felis catus (domestic cat)

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Component #2: protein, cat ACE2

ProteinName: cat ACE2 / Recombinant expression: No

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Component #3: protein, SARS-CoV-2 RBD

ProteinName: SARS-CoV-2 RBD / Recombinant expression: No

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Component #4: protein, Angiotensin-converting enzyme 2

ProteinName: Angiotensin-converting enzyme 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.132953 kDa
SourceSpecies: Felis catus (domestic cat)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Spike protein S1

ProteinName: Spike protein S1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.873496 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle
Sample solutionpH: 8
VitrificationCryogen name: NONE

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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: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 195370
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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