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- PDB-9q3u: Cryo EM structure of elk ACE2 in complex with SARS-CoV-2 spike trimer -

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Basic information

Entry
Database: PDB / ID: 9q3u
TitleCryo EM structure of elk ACE2 in complex with SARS-CoV-2 spike trimer
Components
  • Angiotensin-converting enzyme 2
  • Spike protein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Cervidae / ACE2 receptor / viral host interaction / host susceptibility
Biological speciesCervus canadensis (elk)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 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: Nat Commun / Year: 2026
Title: Species- and variant-specific ACE2 compatibility shapes SARS-CoV-2 spillover potential in North American cervids.
Authors: Constanza Espada / Kai Ye / Yingyi Long / Kritika Pasai / Thomas J DeLiberto / Jonathon Heale / Riley Wiese / Qiongying Yang / Mingyi Zhou / Sean Streich / Yizhi Jane Tao / Jeffrey C Chandler / Xiu-Feng Wan /
Abstract: Free-ranging white-tailed deer (WTD) are established SARS-CoV-2 reservoirs, but the susceptibility of other cervid species remains unclear. Here we integrate receptor analysis, structural modeling, ...Free-ranging white-tailed deer (WTD) are established SARS-CoV-2 reservoirs, but the susceptibility of other cervid species remains unclear. Here we integrate receptor analysis, structural modeling, and field surveillance to assess SARS-CoV-2 susceptibility across North American cervids. We identify species- and variant-specific differences in ACE2-spike compatibility. Elk ACE2 exhibits weak binding to the ancestral strain (Wuhan-Hu-1) and Delta spike receptor-binding domains (RBDs), likely due to a unique K31N substitution. In contrast, it shows stronger binding to Alpha, Beta, Gamma, and Omicron RBDs containing N501Y. Biophysical assays, gel filtration chromatography, and cryo-EM confirm stable complex formation between elk ACE2 and Alpha RBD, but not RBD from the ancestral strain. Despite weak binding, elk ACE2 supports viral entry and replication in vitro. However, surveillance revealed limited evidence of infection in the United States, contrasting with widespread WTD transmissions. These findings demonstrate that ACE2 compatibility alone is insufficient to predict reservoir potential and provide a framework for assessing species susceptibility to emerging coronaviruses.
History
DepositionAug 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: 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 2
B: Spike protein
C: Spike protein
D: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,61330
Polymers499,8614
Non-polymers5,75126
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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) / Production host: Cricetulus griseus (Chinese hamster)
References: Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike protein


Mass: 142472.906 Da / Num. of mol.: 3
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)
#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.: 26 / 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
IDNameTypeEntity IDParent-IDSource
1Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike trimerCOMPLEX#1-#20RECOMBINANT
2Elk ACE2 extracellular domainCOMPLEX#11RECOMBINANT
3SARS-CoV-2 omicron XBB1.5 spikeCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Severe acute respiratory syndrome coronavirus 22697049
32Cervus canadensis (elk)1574408
43Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Cricetulus griseus (Chinese hamster)10029
32Cricetulus griseus (Chinese hamster)10029
43Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 7.4 / Details: 1x PBS, pH 7.4
SpecimenEmbedding 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 supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 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: 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 / Num. of real images: 12804

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Processing

EM software
IDNameVersionCategory
1RELION5.0.0particle selection
2PHENIX1.21.2_5419:model refinement
5RELION5.0.0CTF correction
6cryoSPARCCTF correction
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 185400
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51163 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8HFX

8hfx


Accession code: 8HFX / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00231471
ELECTRON MICROSCOPYf_angle_d0.47442775
ELECTRON MICROSCOPYf_dihedral_angle_d4.6544509
ELECTRON MICROSCOPYf_chiral_restr0.0424815
ELECTRON MICROSCOPYf_plane_restr0.0035489

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