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- EMDB-66471: Ra22QT77 RBD in complex with Bat ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-66471
TitleRa22QT77 RBD in complex with Bat ACE2
Map data
Sample
  • Complex: Bat ACE2 Complexed with Ra22QT77 RBD
    • Complex: Bat ACE2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: Ra22QT77 RBD
      • Protein or peptide: Spike glycoprotein
KeywordsCOMPLEX / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / carboxypeptidase activity / peptidyl-dipeptidase activity / metallopeptidase activity / cilium / positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / : / receptor-mediated virion attachment to host cell / host cell surface receptor binding ...Hydrolases; Acting on peptide bonds (peptidases) / carboxypeptidase activity / peptidyl-dipeptidase activity / metallopeptidase activity / cilium / positive regulation of viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / : / receptor-mediated virion attachment to host cell / host cell surface receptor binding / 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 / metal ion binding / membrane / identical protein 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. / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily ...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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesRhinolophus ferrumequinum (greater horseshoe bat) / Rhinolophus ferrumequinum coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsSato S / Matsumoto K / Oshima HS / Akasaka H / Sawada K / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)243fa627001 Japan
CitationJournal: To Be Published
Title: Ra22QT77 RBD in complex with Bat ACE2
Authors: Sato S / Akasaka H / Nureki O
History
DepositionOct 3, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66471.png

Downloads & links

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Map

FileDownload / File: emd_66471.map.gz / Format: CCP4 / Size: 103 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 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å		1 Å/pix.
x 300 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-1.1971312 - 1.5232161
Average (Standard dev.)0.00020447462 (±0.018583842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66471_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66471_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 : Bat ACE2 Complexed with Ra22QT77 RBD

EntireName: Bat ACE2 Complexed with Ra22QT77 RBD
Components
  • Complex: Bat ACE2 Complexed with Ra22QT77 RBD
    • Complex: Bat ACE2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: Ra22QT77 RBD
      • Protein or peptide: Spike glycoprotein

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Supramolecule #1: Bat ACE2 Complexed with Ra22QT77 RBD

SupramoleculeName: Bat ACE2 Complexed with Ra22QT77 RBD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rhinolophus ferrumequinum (greater horseshoe bat)

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Supramolecule #2: Bat ACE2

SupramoleculeName: Bat ACE2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rhinolophus ferrumequinum (greater horseshoe bat)

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Supramolecule #3: Ra22QT77 RBD

SupramoleculeName: Ra22QT77 RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Rhinolophus ferrumequinum coronavirus

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Rhinolophus ferrumequinum (greater horseshoe bat)
Molecular weightTheoretical: 69.159836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEDRAKIF LDNFNHEAED LSYQSSLASW EYNTNISDEN VQKMDEAGAK WSAFYEEQSK LAKNYPLEEI QTVPVKLQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCKPNN PQECFLLEPG LDNIMGTSKD YNERLWAWEG WRAEVGKQLR P LYEEYVAL ...String:
STTEDRAKIF LDNFNHEAED LSYQSSLASW EYNTNISDEN VQKMDEAGAK WSAFYEEQSK LAKNYPLEEI QTVPVKLQLQ ILQQSGSPV LSEDKSKRLN SILNAMSTIY STGKVCKPNN PQECFLLEPG LDNIMGTSKD YNERLWAWEG WRAEVGKQLR P LYEEYVAL KNEMARGYHY EDYGDYWRRD YETEESSGSG YSRDQLMKDV DRIFTEIKPL YEHLHAYVRT KLMDTYPFHI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD AMVNQGWDAN RIFKEAEKFF VSVGLPNMTE GFWNNSMLTE PGD GRKVVC HPTAWDLGKG DFRIKMCTKV TMEDFLTAHH EMGHIQYDMA YATQPYLLRN GANEGFHEAV GEVMSLSVAT PKHL KTMGL LSPDFLEDNE TEINFLLKQA LNIVGTLPFT YMLEKWRWMV FRGEIPKEEW MKKWWEMKRD LVGVVEPVPH DETYC DPAS LFHVANDYSF IRYYTRTIFE FQFHEALCRI AQHDGPLHKC DISNSTDAGK KLHQMLSVGK SQPWTVTLKD IVDSRN MDV GPLLRYFEPL YTWLQEQNRK SYVGWNTDWS P

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Details: Ra22QT77 RBD / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhinolophus ferrumequinum coronavirus
Molecular weightTheoretical: 20.020426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NLCPFGEVFN ATTFASVYAW NRRRISNCVA DYSVLYNTTS FSTFKCYGVS PTKLNDLCFT NVYADSFVVR GDEVRQIAPG QTGKIADYN YKLPDDFMGC VIAWNSISLD AGGSYYYRLF RKSVLKPFER DISTQLYQAG DTPCSVAGPD CYYPLQSYYF Q STNGVGYQ PYRVVVLSF

UniProtKB: Spike glycoprotein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 468116
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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