[English] 日本語
Yorodumi
- EMDB-65720: Rhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65720
TitleRhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 Sarbecovirus Spike RBDs.
Map data
Sample
  • Complex: Sarbecovirus Rc-o319 RBD in complex with Rhinolophus cornutus Bat ACE2
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsthe complex between sarbecovirus RBD and dimeric ACE2 / 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 / cilium / apical plasma membrane / proteolysis / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesRc-o319 (virus) / Sarbecovirus / Rhinolophus cornutus (Little Japanese Horseshoe Bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang J / Li ZX / Li ZM / Hang Y / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82341085 China
CitationJournal: To Be Published
Title: The complex between sarbecovirus Rc-o319-RBD and R.cor bat ACE2
Authors: Wang J / Xiong X
History
DepositionAug 5, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65720.png

Downloads & links

-
Map

FileDownload / File: emd_65720.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.357 Å		0.85 Å/pix.
x 320 pix.
= 271.357 Å		0.85 Å/pix.
x 320 pix.
= 271.357 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84799 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.030834485 - 1.5599554
Average (Standard dev.)0.0011101601 (±0.019993396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.35678 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_65720_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65720_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sarbecovirus Rc-o319 RBD in complex with Rhinolophus cornutus Bat ACE2

EntireName: Sarbecovirus Rc-o319 RBD in complex with Rhinolophus cornutus Bat ACE2
Components
  • Complex: Sarbecovirus Rc-o319 RBD in complex with Rhinolophus cornutus Bat ACE2
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Sarbecovirus Rc-o319 RBD in complex with Rhinolophus cornutus Bat ACE2

SupramoleculeName: Sarbecovirus Rc-o319 RBD in complex with Rhinolophus cornutus Bat ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rc-o319 (virus)

-
Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sarbecovirus / Strain: Rc-o319
Molecular weightTheoretical: 24.40116 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPQDTVVR FPNITNLCPF SEVFNATTFA SVYAWNRKRI SNCVADYSVL YNSTSFSTFQ CYGVSSTKLN DLCFTNVYAD SFVVRGDEV RQIAPGQTGV IADYNYKLPD DFTGCVLAWN SRNQDASTSG NFNYYYRIWR SEKLRPFERD IAHYDYQVGT Q FKSSLKNY ...String:
RVQPQDTVVR FPNITNLCPF SEVFNATTFA SVYAWNRKRI SNCVADYSVL YNSTSFSTFQ CYGVSSTKLN DLCFTNVYAD SFVVRGDEV RQIAPGQTGV IADYNYKLPD DFTGCVLAWN SRNQDASTSG NFNYYYRIWR SEKLRPFERD IAHYDYQVGT Q FKSSLKNY GFYSSAGDSH QPYRVVVLSF ELLNAPATVC GPKQSTELIK NKCVNF

-
Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Rhinolophus cornutus (Little Japanese Horseshoe Bat)
Molecular weightTheoretical: 84.844648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSSWLLLS LVAVTAAQST TEDEAKKFLN DFNSEAENLT YQSSLASWDY NTNISDENVQ KMDEAGAKWS AFYEEQSKIA KNYPLEEIQ TDIVKRQLQI LQQSGSPVLS EDKSKRLNSI LNAMSTIYST GKVCKPNNPQ ECLLLEPGLD NIMGTSKDYH E RLWAWEGW ...String:
MSGSSWLLLS LVAVTAAQST TEDEAKKFLN DFNSEAENLT YQSSLASWDY NTNISDENVQ KMDEAGAKWS AFYEEQSKIA KNYPLEEIQ TDIVKRQLQI LQQSGSPVLS EDKSKRLNSI LNAMSTIYST GKVCKPNNPQ ECLLLEPGLD NIMGTSKDYH E RLWAWEGW RAEVGKQLRP LYEEYVVLKN EMARGYHYED YGDYWRRDYE TEESSGPGYS RDQLMKDVDR IFTEIKPLYE HL HAYVRAK LMDTYPLHIS PTGCLPAHLL GDMWGRFWTN LYPLTVPFGQ KPNIDVTDEM VKQGWDANRI FKEAEKFFVS VGL PNMTEG FWNNSMLTEP GDGRKVVCHP TAWDLGKGDF RIKMCTKVTM EDFLTAHHEM GHIQYDMAYA SQPYLLRNGA NEGF HEAVG EVMSLSVATP KHLKTMGLLS PDFREDDETE INFLLKQALN IVGTLPFTYM LEKWRWMVFK GEIPKEEWMK KWWEM RREI VGVVEPVPHD ETYCDPASLF HVANDYSFIR YYTRTIFEFQ FHEALCRIAQ HNGPLHKCDI SNSTDAGKKL HQMLSV GKS QAWTKTLEDI VGSRNMDVGP LLRYFEPLYT WLQEQNRKSY VGWNTDWSPY SDQSIKVRIS LKSALGEKAY EWNDNEM YL FRSSVAYAMR EYFLKTKNQT ILFGDENVWV SNLKPRISFN FHVTSPENVS DIIPRSEVEG AIRMSRSRIN DAFRLDDN S LEFLGIQPTL

UniProtKB: Angiotensin-converting enzyme

-
Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / 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
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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 987814
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