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- PDB-9q3v: Cryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD -

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Basic information

Entry
Database: PDB / ID: 9q3v
TitleCryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD
Components
  • Angiotensin-converting enzyme 2
  • Spike protein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Cervidae / ACE2 receptor / viral host interaction / host susceptibility
Biological speciesSevere acute respiratory syndrome coronavirus 2
Cervus canadensis (elk)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYe, K. / Tao, Y.J. / Wan, X.F.
Funding support United States, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA) United States
Robert A. Welch Foundation United States
CitationJournal: To Be Published
Title: Species- and variant-specific ACE2 compatibility shapes SARS-CoV-2 spillover potential in North American cervids
Authors: Espada, C. / Ye, K. / Long, Y. / Pasai, K. / DeLiberto, T.J. / Heale, J. / Wiese, R. / Yang, Q. / Zhou, M. / Streich, S. / Tao, Y.J. / Chandler, J.C. / Wan, X.F.
History
DepositionAug 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Spike protein
A: Angiotensin-converting enzyme 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4876
Polymers97,6022
Non-polymers8854
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 Spike protein


Mass: 25159.553 Da / Num. of mol.: 1 / Fragment: RNA binding domain
Source method: isolated from a genetically manipulated source
Details: Author stated the sequence reference should be GB XBC18596.1
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Strain: omicron / Gene: S, 2 / Variant: XBB1.5 / Production host: Cricetulus griseus (Chinese hamster)
#2: Protein Angiotensin-converting enzyme 2


Mass: 72442.500 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Details: Author stated the sequence reference should be GB XP_043314478.1
Source: (gene. exp.) Cervus canadensis (elk) / Gene: ACE2 / Production host: Cricetulus griseus (Chinese hamster)
References: Hydrolases; Acting on peptide bonds (peptidases)
#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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBDCOMPLEXThis complex is from local refinement of the elk ACE2:spike complex#1-#20RECOMBINANT
2Elk ACE2 extracellular domainCOMPLEX#21RECOMBINANT
3Receptor binding domain of SARS-CoV-2 XBB1.5 spike proteinCOMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.105 kDa/nmNO
210.07 MDaYES
310.035 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Severe acute respiratory syndrome coronavirus 22697049XBB1.5
22Cervus canadensis (elk)1574408
33Severe acute respiratory syndrome coronavirus2901879
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Cricetulus griseus (Chinese hamster)10029
22Cricetulus griseus (Chinese hamster)10029
33Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 7.4 / Details: 1x PBS, pH 7.4
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Elk ACE2 and SARS-CoV-2 omicron XBB1.5 spike protein samples were mixed at a 3:1 molar ratio at 1.8 mg/ml total protein concentration for 2 hr at 4 oC.
Specimen supportDetails: The grids were glow discharged with the current set to be 30 mA.
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3

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Processing

EM software
IDNameVersionCategory
1RELION5.0.0particle selection
4RELION5.0.0CTF correction
5cryoSPARCCTF correction
8PHENIX1.21.2_5419:model fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIX1.21.2_5419:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121345 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 7 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 8HFY

8hfy


Accession code: 8HFY / Source name: PDB / Type: experimental model

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