[English] 日本語
Yorodumi
- EMDB-60559: Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60559
TitleRa9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spike RBDs.
Map data
Sample
  • Organelle or cellular component: Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spike RBDs.
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsthe complex between sarbecovirus RBD and bACE2-dimer / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular space / metal ion binding / membrane / cytoplasm
Similarity search - Function
Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily ...Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesBtKY72 (virus) / Kenya bat coronavirus BtKY72 / Rhinolophus affinis (intermediate horseshoe bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang J / Xiong X
Funding support China, 2 items
OrganizationGrant numberCountry
Other governmentSRPG22-002 China
Other government2022A1515110495 China
CitationJournal: Sci Adv / Year: 2025
Title: SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding.
Authors: Jingjing Wang / Yong Ma / Zimu Li / Hang Yuan / Banghui Liu / Zexuan Li / Mengzhen Su / Gul Habib / Yutong Liu / Lutang Fu / Peiyi Wang / Mei Li / Jun He / Jing Chen / Peng Zhou / Zhengli ...Authors: Jingjing Wang / Yong Ma / Zimu Li / Hang Yuan / Banghui Liu / Zexuan Li / Mengzhen Su / Gul Habib / Yutong Liu / Lutang Fu / Peiyi Wang / Mei Li / Jun He / Jing Chen / Peng Zhou / Zhengli Shi / Xinwen Chen / Xiaoli Xiong /
Abstract: High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)-related coronaviruses (SARSr-CoVs) remains ...High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)-related coronaviruses (SARSr-CoVs) remains incompletely understood. We report cryo-electron microscopy structures of eight different S-proteins from SARSr-CoVs found across Asia, Europe, and Africa. These S-proteins all adopt tightly packed, locked, prefusion conformations. These structures enable the classification of SARSr-CoV S-proteins into three types, based on their receptor-binding motif (RBM) structures and ACE2 binding characteristics. Type-2 S-proteins often preferentially bind bat ACE2 (bACE2) over hACE2. We report a structure of a type-2 BtKY72-RBD in complex with bACE2 to understand ACE2 specificity. Structure-guided mutagenesis of BtKY72-RBD reveals that multiple synergistic mutations in four different regions of RBM are required to achieve high-affinity hACE2 binding. Similar RBM changes can also confer hACE2 binding to another type-2 BM48-31 S-protein, which is primarily non-ACE2 binding. These results provide an understanding of how high-affinity hACE2 binding may be acquired by SARSr-CoV S-proteins.
History
DepositionJun 16, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60559.png

Downloads & links

-
Map

FileDownload / File: emd_60559.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.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.052547242 - 0.150777
Average (Standard dev.)0.0006816291 (±0.00474816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60559_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60559_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spi...

EntireName: Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spike RBDs.
Components
  • Organelle or cellular component: Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spike RBDs.
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spi...

SupramoleculeName: Ra9479 Bat ACE2 Dimer in Complex with Two BtKY72 Sarbecovirus Spike RBDs.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: BtKY72 (virus)

-
Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1
Details: Sequence reference for source organism Kenya bat coronavirus BtKY72 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3Q8AKM0.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Kenya bat coronavirus BtKY72
Molecular weightTheoretical: 24.222271 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVSPSTEVVR FPNITNLCPF GQVFNASNFP SVYAWERLRI SDCVADYAVL YNSSSSFSTF KCYGVSPTKL NDLCFSSVYA DYFVVKGDD VRQIAPAQTG VIADYNYKLP DDFTGCVLAW NTNSVDSKSG NNFYYRLFRH GKIKPYERDI SNVLYNSAGG T CSSISQLG ...String:
RVSPSTEVVR FPNITNLCPF GQVFNASNFP SVYAWERLRI SDCVADYAVL YNSSSSFSTF KCYGVSPTKL NDLCFSSVYA DYFVVKGDD VRQIAPAQTG VIADYNYKLP DDFTGCVLAW NTNSVDSKSG NNFYYRLFRH GKIKPYERDI SNVLYNSAGG T CSSISQLG CYEPLKSYGF TPTVGVGYQP YRVVVLSFEL LNAPATVCGP KKSTELVKNK

UniProtKB: Spike glycoprotein

-
Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Details: thrombin cleavage site His-tag / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Rhinolophus affinis (intermediate horseshoe bat)
Molecular weightTheoretical: 86.143156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSSWLLLS LVAVTAAQST TEDRAKIFLD NFNHEAEDLS YQSSLASWEY NTNISDENVQ KMDEAGAKWS AFYEEQSKLA KNYPLEEIQ TVPVKLQLQI LQQSGSPVLS EDKSKRLNSI LNAMSTIYST GKVCKPNNPQ ECFLLEPGLD NIMGTSKDYN E RLWAWEGW ...String:
MSGSSWLLLS LVAVTAAQST TEDRAKIFLD NFNHEAEDLS YQSSLASWEY NTNISDENVQ KMDEAGAKWS AFYEEQSKLA KNYPLEEIQ TVPVKLQLQI LQQSGSPVLS EDKSKRLNSI LNAMSTIYST GKVCKPNNPQ ECFLLEPGLD NIMGTSKDYN E RLWAWEGW RAEVGKQLRP LYEEYVVLKN EMARGYHYED YGDYWRRDYE TEESSGSGYS RDQLMKDVDR IFTEIKPLYE HL HAYVRTK LMDTYPFHIS PTGCLPAHLL GDMWGRFWTN LYPLTVPFGQ KPNIDVTDAM VNQGWDANRI FKEAEKFFVS VGL PNMTEG FWNNSMLTEP GDGRKVVCHP TAWDLGKGDF RIKMCTKVTM EDFLTAHHEM GHIQYDMAYA TQPYLLRNGA NEGF HEAVG EVMSLSVATP KHLKTMGLLS PDFLEDNETE INFLLKQALN IVGTLPFTYM LEKWRWMVFR GEIPKEEWMK KWWEM KRDL VGVVEPVPHD ETYCDPASLF HVANDYSFIR YYTRTIFEFQ FHEALCRIAQ HDGPLHKCDI SNSTDAGKKL HQMLSV GKS QPWTVTLKDI VDSRNMDVGP LLRYFEPLYT WLQEQNRKSH VGWNTDWSPY SDQSIKVRIS LKSALGEKAY EWNDNEM YL FRSSVAYAMR EYFSKKNQPI LFGVENVWVS NLKPRISFNF HVTSPGNVSD IIPRSEVEGA IRMSRSRIND AFRLDDNS L EFLGIQPTLG LVPRGSGHHH HHH

UniProtKB: Angiotensin-converting enzyme

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4disodium hydrogen phosphate
1.8 mMKH2PO4potassium dihydrogen phosphate

Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m17

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 931804
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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