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- EMDB-62524: The RBD of HKU5 complex with Pipistrellus abramus ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-62524
TitleThe RBD of HKU5 complex with Pipistrellus abramus ACE2
Map data
Sample
  • Complex: The RBD of HKU5 complex with Pipistrellus abramus ACE2
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHKU5 / VIRAL PROTEIN
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 (S) protein S1 subunit, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / 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, receptor-binding domain, MERS-CoV-like / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / 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. / 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. / 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 speciesBat coronavirus HKU5 / Pipistrellus abramus (Japanese house bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZhang YY / Xia LY / Zhou Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82241081 China
CitationJournal: To Be Published
Title: Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5
Authors: Zhang YY / Xia LY / Zhou Q
History
DepositionNov 27, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62524.png

Downloads & links

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Map

FileDownload / File: emd_62524.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.1568294 - 5.6576004
Average (Standard dev.)0.00470453 (±0.14528458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62524_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_62524_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 : The RBD of HKU5 complex with Pipistrellus abramus ACE2

EntireName: The RBD of HKU5 complex with Pipistrellus abramus ACE2
Components
  • Complex: The RBD of HKU5 complex with Pipistrellus abramus ACE2
    • 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: The RBD of HKU5 complex with Pipistrellus abramus ACE2

SupramoleculeName: The RBD of HKU5 complex with Pipistrellus abramus ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bat coronavirus HKU5

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bat coronavirus HKU5
Molecular weightTheoretical: 22.022654 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TQECDFTPML TGTPPPIYNF KRLVFTNCNY NLTKLLSLFQ VSEFSCHQVS PSSLATGCYS SLTVDYFAYS TDMSSYLQPG SAGAIVQFN YKQDFSNPTC RVLATVPQNL TTITKPSNYA YLTECYKTSA YGKNYLYNAP GAYTPCLSLA SRGFSTKYQS H SDGELTTT ...String:
TQECDFTPML TGTPPPIYNF KRLVFTNCNY NLTKLLSLFQ VSEFSCHQVS PSSLATGCYS SLTVDYFAYS TDMSSYLQPG SAGAIVQFN YKQDFSNPTC RVLATVPQNL TTITKPSNYA YLTECYKTSA YGKNYLYNAP GAYTPCLSLA SRGFSTKYQS H SDGELTTT GYIYPVTGNL QMAFIISVQY GTDTNSVCPM Q

UniProtKB: Spike glycoprotein

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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: Pipistrellus abramus (Japanese house bat)
Molecular weightTheoretical: 92.874102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSSWLLLS LVAVAGAQYT TEEEARRFLV KFNHEAENLS HESALASWDY NTNITDENAK KMNEADNKWS DFYKEQSKIA QGFPLQEIK DPIIKLQLQI LQQNGSSVLT AEKRKRLSTI LTTMSTIYST GKVCNPNNPQ QCFTLSGLED IMEKSKDYHE R LWVWEGWR ...String:
MSSSSWLLLS LVAVAGAQYT TEEEARRFLV KFNHEAENLS HESALASWDY NTNITDENAK KMNEADNKWS DFYKEQSKIA QGFPLQEIK DPIIKLQLQI LQQNGSSVLT AEKRKRLSTI LTTMSTIYST GKVCNPNNPQ QCFTLSGLED IMEKSKDYHE R LWVWEGWR SEVGKQLRPL YEEYVELKNE MARGNNYKDY GDYWRGDYET EGEKGYNYSR NYLMEDVDRI FLEIKPLYEQ LH AYVRAKL MKAYPSHISP TGCLPAHLLG DMWGRFWTNL YNLTVPLEKE PNIDVTDTMK KQSWDAEKIF KEAEKFYSSV GLP NMTPGF WRDSMLTEPS DGRQVVCHPT AWDLGKNDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAN QSYLLRNGAN EGFH EAVGE VMSLSVATPK HLKGMGLLPS DFSENNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFEG KIPKEQWMEK WWEMK REIV GVVEPLPHDE TYCDPASLFH VANDYSFIRY FTRTILEFQF QEALCRTAKH QGPLHKCDIS NSTEAGKKLN DMLKLG KST PWTYALEKIA ETKEMDAKPL LNYFNPLFRW LKEQNGNSVG WSVDSSPYSN QSIKVRISLK SALGEKAYEW NENEMYL FQ SSVAYAMRVY FLKAKNESIP FRAEDVRVSD EKKRVSFKFF VTSPTNMSDI IPRSEVEDAI RMSRSRINDA FRLDDNTL E FLGVQPTLGP PYQPPVTIWL IVFGVVMGVV VIGIGVLIFT GIRDRKKRNQ AENEENPYSS VNLSKGENNP GFQSGDDVQ TSF

UniProtKB: Angiotensin-converting enzyme

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.6.0) / Number images used: 40837
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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