[English] 日本語
Yorodumi
- EMDB-30305: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30305
TitleCryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Map dataCryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Sample
  • Complex: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
    • Complex: cat ACE2
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 RBD
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
Function / homology
Function and homology information


angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release ...angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / membrane => GO:0016020 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesFelis catus (domestic cat) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / Resolution: 3.0 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.
History
DepositionMay 29, 2020-
Header (metadata) releaseSep 2, 2020-
Map releaseSep 2, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBj / Status: Released

-
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
  • Download
  • 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

emd_30305.png

Downloads & links

-
Map

FileDownload / File: emd_30305.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
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

-
Supplemental data

-
Sample components

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

EntireName: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
Components
  • Complex: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD
    • Complex: cat ACE2
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 RBD
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION

-
Supramolecule #1: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD

SupramoleculeName: Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Felis catus (domestic cat)

-
Supramolecule #2: cat ACE2

SupramoleculeName: cat ACE2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

-
Supramolecule #3: SARS-CoV-2 RBD

SupramoleculeName: SARS-CoV-2 RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: angiotensin-converting enzyme 2
Source (natural)Organism: Felis catus (domestic cat)
Molecular weightTheoretical: 85.132953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQSTTEELAK TFLEKFNHEA EELSYQSSLA SWNYNTNITD ENVQKMNEAG AKWSAFYEEQ SKLAKTYPLA EIHNTTVKRQ LQALQQSGS SVLSADKSQR LNTILNAMST IYSTGKACNP NNPQECLLLE PGLDDIMENS KDYNERLWAW EGWRAEVGKQ L RPLYEEYV ...String:
MQSTTEELAK TFLEKFNHEA EELSYQSSLA SWNYNTNITD ENVQKMNEAG AKWSAFYEEQ SKLAKTYPLA EIHNTTVKRQ LQALQQSGS SVLSADKSQR LNTILNAMST IYSTGKACNP NNPQECLLLE PGLDDIMENS KDYNERLWAW EGWRAEVGKQ L RPLYEEYV ALKNEMARAN NYEDYGDYWR GDYEEEWTDG YNYSRSQLIK DVEHTFTQIK PLYQHLHAYV RAKLMDTYPS RI SPTGCLP AHLLGDMWGR FWTNLYPLTV PFGQKPNIDV TDAMVNQSWD ARRIFKEAEK FFVSVGLPNM TQGFWENSML TEP GDSRKV VCHPTAWDLG KGDFRIKMCT KVTMDDFLTA HHEMGHIQYD MAYAVQPFLL RNGANEGFHE AVGEIMSLSA ATPN HLKTI GLLSPGFSED SETEINFLLK QALTIVGTLP FTYMLEKWRW MVFKGEIPKE QWMQKWWEMK REIVGVVEPV PHDET YCDP ASLFHVANDY SFIRYYTRTI YQFQFQEALC RIAKHEGPLH KCDISNSSEA GKKLLQMLTL GKSKPWTLAL EHVVGE KKM NVTPLLKYFE PLFTWLKEQN RNSFVGWNTD WRPYADQSIK VRISLKSALG DEAYEWNDNE MYLFRSSVAY AMREYFS KV KNQTIPFVED NVWVSNLKPR ISFNFFVTAS KNVSDVIPRS EVEEAIRMSR SRINDAFRLD DNSLEFLGIQ PTLSPPYQ P PVTHHHHHHH H

-
Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.873496 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGP

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195370
Image recording ID1
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more