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- PDB-9yej: Structure of mink-derived HKU5 RBD in complex with ACE2 of N. vison -

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Basic information

Entry
Database: PDB / ID: 9yej
TitleStructure of mink-derived HKU5 RBD in complex with ACE2 of N. vison
Components
  • Angiotensin-converting enzyme
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / Immune system / ACE2 / mink HKU5 / bat coronavirus
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / carboxypeptidase activity / peptidyl-dipeptidase activity / metallopeptidase activity / cilium / apical plasma membrane / proteolysis / extracellular region / 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 speciesNeogale vison (American mink)
Pipistrellus bat coronavirus HKU5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, N. / Keeler, E. / Tsybovsky, Y. / 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: To Be Published
Title: Adaptation to intermediate 1 host expands zoonotic risk of bat-origin merbecoviruses
Authors: Keeler, E.L. / Li, N. / Arinola, R. / Teng, I. / Grunst, M.W. / Kaur, R. / Zepeda, S. / Okten, A. / Menasche, B. / Catanzaro, N.J. / Young, S. / Bourgikos, E. / Grubaugh, N. / Mothes, W. / ...Authors: Keeler, E.L. / Li, N. / Arinola, R. / Teng, I. / Grunst, M.W. / Kaur, R. / Zepeda, S. / Okten, A. / Menasche, B. / Catanzaro, N.J. / Young, S. / Bourgikos, E. / Grubaugh, N. / Mothes, W. / Baric, R.S. / Spaulding, A.B. / Serebryannyy, L. / Jangra, R.K. / Tsybovsky, Y. / Alfajaro, M.M. / Zhou, T. / Douek, D.C. / Wilen, C.B.
History
DepositionSep 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: 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)488,55411
Polymers487,0064
Non-polymers1,5487
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: 93301.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neogale vison (American mink) / Cell line (production host): EXPI / Production host: Homo sapiens (human)
References: UniProt: A0A7T0Q2W2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike glycoprotein


Mass: 150201.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pipistrellus bat coronavirus HKU5 / Production host: Homo sapiens (human)
#3: 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.: 7 / 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: Mink HKU5 RBD in complex with mink ACE2 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.16 MDa / Experimental value: NO
Source (natural)Organism: Neogale vison (American mink)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 4.3 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: 11322
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2Topazparticle selection
3SerialEM4.1.6image acquisition
5cryoSPARC4.6CTF correction
8UCSF ChimeraXmodel fitting
9Coot0.9.8.7model fitting
11PHENIX1.21.1_5286model refinement
12ISOLDEmodel refinement
13cryoSPARC4.6initial Euler assignment
14cryoSPARC4.6final Euler assignment
15cryoSPARCclassification
16cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3031602
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 418147 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215090
ELECTRON MICROSCOPYf_angle_d0.53920489
ELECTRON MICROSCOPYf_dihedral_angle_d4.9452130
ELECTRON MICROSCOPYf_chiral_restr0.0412167
ELECTRON MICROSCOPYf_plane_restr0.0032647

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