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- EMDB-61517: BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-61517
TitleBtHKU5-CoV-2-441 Spike RBD domain binding to hACE2
Map data
Sample
  • Complex: BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: BtHKU5-CoV-2-441 Spike RBD domain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsRBD-receptor Complex / Virus Entry / Zoonotic / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / cilium / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane
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. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesPipistrellus bat coronavirus HKU5 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsZhang W / Peng W / Chen HY
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2023YFC2605500 China
CitationJournal: Cell / Year: 2025
Title: Bat-infecting merbecovirus HKU5-CoV lineage 2 can use human ACE2 as a cell entry receptor.
Authors: Jing Chen / Wei Zhang / Yang Li / Chen Liu / Tianyi Dong / Huiyu Chen / Chunguang Wu / Jia Su / Bei Li / Wei Zhang / Ben Hu / Jingkun Jia / Cheng-Bao Ma / Yan Zhu / Xiangyang He / Ang Li / ...Authors: Jing Chen / Wei Zhang / Yang Li / Chen Liu / Tianyi Dong / Huiyu Chen / Chunguang Wu / Jia Su / Bei Li / Wei Zhang / Ben Hu / Jingkun Jia / Cheng-Bao Ma / Yan Zhu / Xiangyang He / Ang Li / Kaiyi Pan / Haofeng Lin / Zishuo Guo / Cong Li / Libiao Zhang / Huan Yan / Peng Zhou / Wei Peng / Zheng-Li Shi /
Abstract: Merbecoviruses comprise four viral species with remarkable genetic diversity: MERS-related coronavirus, Tylonycteris bat coronavirus HKU4, Pipistrellus bat coronavirus HKU5, and Hedgehog coronavirus ...Merbecoviruses comprise four viral species with remarkable genetic diversity: MERS-related coronavirus, Tylonycteris bat coronavirus HKU4, Pipistrellus bat coronavirus HKU5, and Hedgehog coronavirus 1. However, the potential human spillover risk of animal merbecoviruses remains to be investigated. Here, we reported the discovery of HKU5-CoV lineage 2 (HKU5-CoV-2) in bats that efficiently utilize human angiotensin-converting enzyme 2 (ACE2) as a functional receptor and exhibits a broad host tropism. Cryo-EM analysis of HKU5-CoV-2 receptor-binding domain (RBD) and human ACE2 complex revealed an entirely distinct binding mode compared with other ACE2-utilizing merbecoviruses with RBD footprint largely shared with ACE2-using sarbecoviruses and NL63. Structural and functional analyses indicate that HKU5-CoV-2 has a better adaptation to human ACE2 than lineage 1 HKU5-CoV. Authentic HKU5-CoV-2 infected human ACE2-expressing cell lines and human respiratory and enteric organoids. This study reveals a distinct lineage of HKU5-CoVs in bats that efficiently use human ACE2 and underscores their potential zoonotic risk.
History
DepositionSep 13, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61517.png

Downloads & links

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Map

FileDownload / File: emd_61517.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.)
0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å		0.73 Å/pix.
x 320 pix.
= 233.6 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.0357733 - 1.5094889
Average (Standard dev.)0.000272657 (±0.02830922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 233.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61517_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61517_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2

EntireName: BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2
Components
  • Complex: BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: BtHKU5-CoV-2-441 Spike RBD domain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2

SupramoleculeName: BtHKU5-CoV-2-441 Spike RBD domain binding to hACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Pipistrellus bat coronavirus HKU5

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Macromolecule #1: BtHKU5-CoV-2-441 Spike RBD domain

MacromoleculeName: BtHKU5-CoV-2-441 Spike RBD domain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pipistrellus bat coronavirus HKU5
Molecular weightTheoretical: 26.368834 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDAMKRGLCC VLLLCGAVFV SAAKSRGKFI EQPKVQECDF SPLLTGTPPQ VYNFNRLSFT NCNYNLTKLL SLFEVSEFSC NAISPSALA STCYSSLTVD YFAFPLSMAS YLRPGSTGPT AEFNYRQDFS NPTCRVLATP SSNITITKPS NYNWIRLCRT T GAFGNRDQ ...String:
MDAMKRGLCC VLLLCGAVFV SAAKSRGKFI EQPKVQECDF SPLLTGTPPQ VYNFNRLSFT NCNYNLTKLL SLFEVSEFSC NAISPSALA STCYSSLTVD YFAFPLSMAS YLRPGSTGPT AEFNYRQDFS NPTCRVLATP SSNITITKPS NYNWIRLCRT T GAFGNRDQ KVQPGHYSRC RYIAPTGSIY LGGNEGYLVS DGQSASMTER VQMTFVISVT FGTESNSVCP AAAHHHHHHH H

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Macromolecule #2: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.472094 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL ...String:
STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL KNEMARANHY EDYGDYWRGD YEVNGVDGYD YSRGQLIEDV EHTFEEIKPL YEHLHAYVRA KLMNAYPSYI SP IGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD AMVDQAWDAQ RIFKEAEKFF VSVGLPNMTQ GFWENSMLTD PGN VQKAVC HPTAWDLGKG DFRILMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LSPDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVSNDYSF IRYYTRTLYQ FQFQEALCQA AKHEGPLHKC DISNSTEAGQ KLFNMLRLGK SEPWTLALEN VVGAKN MNV RPLLNYFEPL FTWLKDQNKN SFVGWSTDWS PYADAAAHHH HHHHH

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 6 / 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 / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zdq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 295590
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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