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- EMDB-65719: Rhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 S... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-65719
TitleRhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 Sarbecovirus Spike RBDs.
Map data
Sample
  • Complex: Rhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 Sarbecovirus Spike RBDs
    • 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: 2.4 Å
AuthorsWang J / Xiong X / Li ZX / Li ZM / Hang Y
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

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Structure visualization

Supplemental images

emd_65719.png

Downloads & links

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Map

FileDownload / File: emd_65719.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0465
Minimum - Maximum-0.099194236 - 0.32712302
Average (Standard dev.)0.00040452144 (±0.008905932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65719_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65719_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 S...

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

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Supramolecule #1: Rhinolophus cornutus Bat ACE2 Dimer in Complex with Two Rc-o319 S...

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

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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

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Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 493907
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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