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- PDB-9mv0: Structure of HKU5 spike C-terminal domain in complex with ACE2 fr... -

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Basic information

Entry
Database: PDB / ID: 9mv0
TitleStructure of HKU5 spike C-terminal domain in complex with ACE2 from Pipistrellus abramus
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / Immune system / ACE2 / bat coronavirus / merbecovirus / HKU5
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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesPipistrellus abramus (Japanese house bat)
Pipistrellus bat coronavirus HKU5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsLi, N. / Tsybovsky, Y. / Teng, I. / Zhou, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2025
Title: HKU5 bat merbecoviruses engage bat and mink ACE2 as entry receptors
Authors: Madel Alfajaro, M. / Keeler, E.L. / Li, N. / Catanzaro, N.J. / Teng, I.T. / Zhao, Z. / Grunst, M.W. / Yount, B. / Schafer, A. / Wang, D. / Kim, A.S. / Synowiec, A. / Pena-Hernandez, M.A. / ...Authors: Madel Alfajaro, M. / Keeler, E.L. / Li, N. / Catanzaro, N.J. / Teng, I.T. / Zhao, Z. / Grunst, M.W. / Yount, B. / Schafer, A. / Wang, D. / Kim, A.S. / Synowiec, A. / Pena-Hernandez, M.A. / Zepeda, S. / Arinola, R. / Kaur, R. / Menasche, B.L. / Wei, J. / Russell, G.A. / Huck, J. / Song, J. / Ring, A. / Iwasaki, A. / Jangra, R.K. / Lee, S. / Martinez, D.R. / Mothes, W. / Uchil, P.D. / Doench, J.G. / Spaulding, A.B. / Baric, R.S. / Serebryannyy, L. / Tsybovsky, Y. / Zhou, T. / Douek, D.C. / Wilen, C.B.
History
DepositionJan 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: Spike glycoprotein
C: Angiotensin-converting enzyme
D: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,84316
Polymers485,3764
Non-polymers3,46712
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Angiotensin-converting enzyme


Mass: 92874.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pipistrellus abramus (Japanese house bat)
Cell line (production host): EXPI / Production host: Homo sapiens (human)
References: UniProt: C7ECT9, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 149814.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pipistrellus bat coronavirus HKU5 / Gene: S, 2 / Cell line (production host): EXPI / Production host: Homo sapiens (human) / References: UniProt: A3EXD0
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ACE2-ACT66266.1 in complex with HKU5-CTD (ABN10875) / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.16 MDa / Experimental value: NO
Source (natural)Organism: Pipistrellus abramus bat coronavirus HKU5-related
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 3.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10702
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2Topazparticle selection
3SerialEM4.1.6image acquisition
5cryoSPARC4.4CTF correction
8UCSF ChimeraXmodel fitting
9Coot0.9.8.7model fitting
11cryoSPARC4.4initial Euler assignment
12cryoSPARC4.4final Euler assignment
13cryoSPARCclassification
14cryoSPARC4.43D reconstruction
21PHENIX1.21.1_5286model refinement
22ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2125866
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242675 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 4.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215034
ELECTRON MICROSCOPYf_angle_d0.52620374
ELECTRON MICROSCOPYf_dihedral_angle_d5.2982282
ELECTRON MICROSCOPYf_chiral_restr0.0372204
ELECTRON MICROSCOPYf_plane_restr0.0032590

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