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- PDB-7c8d: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD -

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Basic information

Entry
Database: PDB / ID: 7c8d
TitleCryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsHYDROLASE/VIRAL PROTEIN / ACE2 / SARS-CoV-2 / Cryo-EM / complex / PROTEIN BINDING / HYDROLASE-VIRAL PROTEIN complex
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 / metallopeptidase activity / virus receptor activity / host cell surface receptor binding / endocytosis involved in viral entry into host cell ...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 / metallopeptidase activity / virus receptor activity / host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 / go:0009405: / host cell plasma membrane / virion membrane / cell surface / extracellular space / integral component of membrane / identical protein binding / plasma membrane / metal ion binding / cytoplasm
Betacoronavirus spike glycoprotein S1, receptor binding / Angiotensin-converting enzyme / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike receptor binding domain superfamily, coronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Collectrin domain / in:ipr027400: / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S2, coronavirus / Peptidase M2, peptidyl-dipeptidase A
Spike glycoprotein / Angiotensin-converting enzyme 2
Biological speciesFelis catus (domestic cat)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3 Å
AuthorsGao, G.F. / Wang, Q.H. / Wu, L.l.
Funding support China, 1items
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 Report
SummaryFull reportAbout validation report
History
DepositionMay 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0723
Polymers107,0062
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2020 Å2
ΔGint-41 kcal/mol
Surface area33420 Å2

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Components

#1: Protein Angiotensin-converting enzyme 2 / / ACE-related carboxypeptidase


Mass: 85132.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: ACE2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q56H28, angiotensin-converting enzyme 2
#2: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein


Mass: 21873.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#3: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBDCOMPLEX#1-#20MULTIPLE SOURCES
2cat ACE2COMPLEX#11MULTIPLE SOURCES
3SARS-CoV-2 RBDCOMPLEX#21MULTIPLE SOURCES
Source (natural)Organism: Felis catus (domestic cat)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150GATAN K3 BIOQUANTUM (6k x 4k)
2150GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195370 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036539
ELECTRON MICROSCOPYf_angle_d0.4818889
ELECTRON MICROSCOPYf_dihedral_angle_d20.728862
ELECTRON MICROSCOPYf_chiral_restr0.04936
ELECTRON MICROSCOPYf_plane_restr0.0041146

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