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- EMDB-72208: Cryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-72208
TitleCryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD
Map data
Sample
  • Complex: Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBD
    • Complex: Elk ACE2 extracellular domain
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: Receptor binding domain of SARS-CoV-2 XBB1.5 spike protein
      • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Cervidae / ACE2 receptor / viral host interaction / host susceptibility / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Cervus canadensis (elk) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYe K / Tao YJ / Wan XF
Funding support United States, 2 items
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 TJ / Heale J / Wiese R / Yang Q / Zhou M / Streich S / Tao YJ / Chandler JC / Wan XF
History
DepositionAug 19, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72208.png

Downloads & links

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Map

FileDownload / File: emd_72208.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 499.2 Å		0.83 Å/pix.
x 600 pix.
= 499.2 Å		0.83 Å/pix.
x 600 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-11.053925 - 13.720136999999999
Average (Standard dev.)-0.0011346205 (±0.037287246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 499.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72208_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72208_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_72208_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBD

EntireName: Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBD
Components
  • Complex: Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBD
    • Complex: Elk ACE2 extracellular domain
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: Receptor binding domain of SARS-CoV-2 XBB1.5 spike protein
      • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBD

SupramoleculeName: Binary complex of elk ACE2 with SARS-CoV-2 XBB 1.5 Spike RBD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: This complex is from local refinement of the elk ACE2:spike complex
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: XBB1.5
Molecular weightTheoretical: 35 KDa

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Supramolecule #2: Elk ACE2 extracellular domain

SupramoleculeName: Elk ACE2 extracellular domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Cervus canadensis (elk)

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Supramolecule #3: Receptor binding domain of SARS-CoV-2 XBB1.5 spike protein

SupramoleculeName: Receptor binding domain of SARS-CoV-2 XBB1.5 spike protein
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Macromolecule #1: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 1
Details: Author stated the sequence reference should be GB XBC18596.1
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: omicron
Molecular weightTheoretical: 25.159553 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: RVQPTESIVR FPNITNLCPF HEVFNATTFA SVYAWNRKRI SNCVADYSVI YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIRGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKPSG NYNYLYRLFR KSKLKPFERD ISTEIYQAGN K PCNGVAGP ...String:
RVQPTESIVR FPNITNLCPF HEVFNATTFA SVYAWNRKRI SNCVADYSVI YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIRGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKPSG NYNYLYRLFR KSKLKPFERD ISTEIYQAGN K PCNGVAGP NCYSPLQSYG FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNF

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Macromolecule #2: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 2
Details: Author stated the sequence reference should be GB XP_043314478.1
Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Cervus canadensis (elk)
Molecular weightTheoretical: 72.4425 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MTGSFWLLLS LVAVTAAQST TEEQAKTFLE NFNHEAEDLS YQSSLASWNY NTNITDENVQ KMNEARAKWS AFYEEQSRMA KTYSLEEIQ NLTLKRQLKA LQQSGTSVLS AEKSKRLNTI LNTMSTIYST GKVLDPNTQE CLALEPGLDD IMENSRDYNR R LWAWEGWR ...String:
MTGSFWLLLS LVAVTAAQST TEEQAKTFLE NFNHEAEDLS YQSSLASWNY NTNITDENVQ KMNEARAKWS AFYEEQSRMA KTYSLEEIQ NLTLKRQLKA LQQSGTSVLS AEKSKRLNTI LNTMSTIYST GKVLDPNTQE CLALEPGLDD IMENSRDYNR R LWAWEGWR AEVGKQLRPL YEEYVVLENE MARANNYEDY GDYWRGDYEV TEAGDYDYSR DQLMKDVEHT FAEIKPLYEQ LH AYVRAKL MDTYPSYISP TGCLPAHLLG DMWGRFWTNL YSLTVPFKHK PSIDVTEKME NQSWDAERIF KEAEKFFVSI GLP HMTQGF WDNSMLTEPG DGRKVVCHPT AWDLGKGDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAA QPYLLRNGAN EGFH EAVGE IMSLSAATPH YLKALGLLEP DFYEDNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFKG EIPKEQWMQK WWEMK REIV GVVEPLPHDE TYCDPACLFH VAEDYSFIRY YTRTIYQFQF HEALCKTAKH EGALFKCDIS NSTEAGQRLL QMLSLG KSE PWTLALESIV GIKTMDVKPL LNYFEPLFTW LKEQNKNSFV GWSTEWTPYS DGGHHHHHH

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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: 4 / 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

Concentration1.8 mg/mL
BufferpH: 7.4 / Details: 1x PBS, pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.05 kPa
Details: The grids were glow discharged with the current set to be 30 mA.
VitrificationCryogen name: ETHANE
DetailsElk 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Average electron dose: 1.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: RELION (ver. 5.0.0), cryoSPARC) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8hfy

Final reconstructionNumber classes used: 7 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121345
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Avg.num./class: 18540 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8hfy


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

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

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