[English] 日本語
Yorodumi
- EMDB-36892: Structure of BtKY72 spike receptor-binding domain (RBD) complexed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36892
TitleStructure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2
Map data
Sample
  • Complex: Structure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2
    • Complex: BtKY72 RBD
      • Protein or peptide: BtKY72
    • Complex: Bat ACE2
      • Protein or peptide: ACE2
  • Ligand: ZINC ION
KeywordsBtKY72 RBD ACE2 bat / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome-related coronavirus / Rhinolophus landeri (Lander's horseshoe bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSu C / Qi JX / Gao GF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: mBio / Year: 2024
Title: Structural characteristics of BtKY72 RBD bound to bat ACE2 reveal multiple key residues affecting ACE2 usage of sarbecoviruses.
Authors: Chao Su / Juanhua He / Liang Wang / Yu Hu / Jian Cao / Bin Bai / Jianxun Qi / George Fu Gao / Mengsu Yang / Qihui Wang /
Abstract: Two different sarbecoviruses, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2, have caused serious challenges to public health. Certain sarbecoviruses utilize angiotensin- ...Two different sarbecoviruses, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2, have caused serious challenges to public health. Certain sarbecoviruses utilize angiotensin-converting enzyme 2 (ACE2) as their cellular receptor, whereas some do not, speculatively due to the two deletions in their receptor-binding domain (RBD). However, it remains unclear whether sarbecoviruses with one deletion in the RBD can still bind to ACE2. Here, we showed that two phylogenetically related sarbecoviruses with one deletion, BtKY72 and BM48-31, displayed a different ACE2-usage range. The cryo-electron microscopy structure of BtKY72 RBD bound to bat ACE2 identified a key residue important for the interaction between RBD and ACE2. In addition, we demonstrated that the mutations involving four types of core residues enabled the sarbecoviruses with deletion(s) to bind to human ACE2 (hACE2) and broadened the ACE2 usage of SARS-CoV-2. Our findings help predict the potential hACE2-binding ability to emerge sarbecoviruses and develop pan-sarbecovirus therapeutic agents.
IMPORTANCE: Many sarbecoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), possess the ability to bind to receptor angiotensin-converting enzyme 2 (ACE2) through their ...IMPORTANCE: Many sarbecoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), possess the ability to bind to receptor angiotensin-converting enzyme 2 (ACE2) through their receptor-binding domain (RBD). However, certain sarbecoviruses with deletion(s) in the RBD lack this capability. In this study, we investigated two closely related short-deletion sarbecoviruses, BtKY72 and BM48-31, and revealed that BtKY72 exhibited a broader ACE2-binding spectrum compared to BM48-31. Structural analysis of the BtKY72 RBD-bat ACE2 complex identifies a critical residue at position 493 contributing to these differences. Furthermore, we demonstrated that the mutations involving four core residues in the RBD enabled the sarbecoviruses with deletion(s) to bind to human ACE2 and expanded the ACE2 usage spectra of SARS-CoV-2. These findings offer crucial insights for accurately predicting the potential threat of newly emerging sarbecoviruses to human health.
History
DepositionJul 20, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36892.png

Downloads & links

-
Map

FileDownload / File: emd_36892.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.)
0.67 Å/pix.
x 360 pix.
= 240.84 Å		0.67 Å/pix.
x 360 pix.
= 240.84 Å		0.67 Å/pix.
x 360 pix.
= 240.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.669 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-1.8936305 - 2.5587635
Average (Standard dev.)-0.0004939009 (±0.049469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 240.84001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_36892_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_36892_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of BtKY72 spike receptor-binding domain (RBD) complexed...

EntireName: Structure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2
Components
  • Complex: Structure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2
    • Complex: BtKY72 RBD
      • Protein or peptide: BtKY72
    • Complex: Bat ACE2
      • Protein or peptide: ACE2
  • Ligand: ZINC ION

-
Supramolecule #1: Structure of BtKY72 spike receptor-binding domain (RBD) complexed...

SupramoleculeName: Structure of BtKY72 spike receptor-binding domain (RBD) complexed with bat ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus

-
Supramolecule #2: BtKY72 RBD

SupramoleculeName: BtKY72 RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rhinolophus landeri (Lander's horseshoe bat)

-
Supramolecule #3: Bat ACE2

SupramoleculeName: Bat ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

-
Macromolecule #1: BtKY72

MacromoleculeName: BtKY72 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus
Molecular weightTheoretical: 25.514703 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 CVNFHHHHHH

-
Macromolecule #2: ACE2

MacromoleculeName: ACE2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus landeri (Lander's horseshoe bat)
Molecular weightTheoretical: 69.443156 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: STPEDLAKTF LDDFNSAAEN LSYQSSLASW EYNTNISDEN IQKMDEAGAK WSDFYETQSK HAKNFSLEEI HNDTVKLQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCRPNN PQECLLLEPG LDNIMGTSKD YNERLWAWEG WRAEVGKQLR P LYEEYVVL ...String:
STPEDLAKTF LDDFNSAAEN LSYQSSLASW EYNTNISDEN IQKMDEAGAK WSDFYETQSK HAKNFSLEEI HNDTVKLQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCRPNN PQECLLLEPG LDNIMGTSKD YNERLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARGYHY EDYGDYWRRD YETEGSPDLE YSRDQLTKDV ERIFAEIKPL YEQLHAYVRA KLMDTYPFHI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD AMLNQTWDAK RIFKEAEKFF VSIGLPHMTE GFWNNSMLTD PGD GRKVVC HPTAWDLGKG DFRIKMCTKV TMEDFLTAHH EMGHIQYDMA YASQPYLLRN GANEGFHEAV GEVMSLSVAT PKHL KTMGL LSPDFLEDNE TEINFLFKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKEEW MTKWWEMKRK IVGVVEPVPH DETYC DPAS LFHVANDYSF IRYYTRTIFE FQFHEALCRI AKHDGPLHKC DISNSTDAGK KLHQMLSVGK SQPWTSVLKD FVDSKD MDV GPLLRYFEPL YTWLKEQNRN SFVGWNTDWS PHAD

-
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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6lzg

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1397414
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