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- EMDB-72207: Cryo EM structure of elk ACE2 in complex with SARS-CoV-2 spike trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-72207
TitleCryo EM structure of elk ACE2 in complex with SARS-CoV-2 spike trimer
Map data
Sample
  • Complex: Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike trimer
    • Complex: Elk ACE2 extracellular domain
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 omicron XBB1.5 spike
      • 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 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_72207.png

Downloads & links

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Map

FileDownload / File: emd_72207.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-1.1936709 - 2.4749978
Average (Standard dev.)-0.0013083109 (±0.04178362)
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_72207_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72207_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72207_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike ...

EntireName: Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike trimer
Components
  • Complex: Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike trimer
    • Complex: Elk ACE2 extracellular domain
      • Protein or peptide: Angiotensin-converting enzyme 2
    • Complex: SARS-CoV-2 omicron XBB1.5 spike
      • Protein or peptide: Spike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike ...

SupramoleculeName: Ternary complex of elk ACE2 with SARS-CoV-2 Omicron XBB1.5 spike trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: Elk ACE2 extracellular domain

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

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Supramolecule #3: SARS-CoV-2 omicron XBB1.5 spike

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

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Macromolecule #1: Angiotensin-converting enzyme 2

MacromoleculeName: Angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1
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 #2: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 2
Details: Author stated the sequence reference should be GB XBC18596.1
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron
Molecular weightTheoretical: 142.472906 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPA LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYQKNNKSWM ESEFRVYSSA N NCTFEYVS ...String:
MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPA LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYQKNNKSWM ESEFRVYSSA N NCTFEYVS QPFLMDLEGK EGNFKNLREF VFKNIDGYFK IYSKHTPINL ERDLPQGFSA LEPLVDLPIG INITRFQTLL AL HRSYLTP VDSSSGWTAG AAAYYVGYLQ PRTFLLKYNE NGTITDAVDC ALDPLSETKC TLKSFTVEKG IYQTSNFRVQ PTE SIVRFP NITNLCPFHE VFNATTFASV YAWNRKRISN CVADYSVIYN FAPFFAFKCY GVSPTKLNDL CFTNVYADSF VIRG NEVSQ IAPGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKPSGNY NYLYRLFRKS KLKPFERDIS TEIYQAGNKP CNGVA GPNC YSPLQSYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTESNKK FLPFQQ FGR DIADTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVPVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEYV NNSYECDIPI GAGICASYQT QTKSHRRARS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTT E ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQ ILPDPSKPSK RSFIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGAA LQIPFAMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLSSTAS ALGKLQDVVN HNAQALNTLV K QLSSKFGA ISSVLNDILS RLDKVEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CG KGYHLMS FPQSAPHGVV FLHVTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSG NCDVVI GIVNNTVYDP LQPELDSFKE ELDKYFKNHT SPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL QELG KYEQG SGYIPEAPRD GQAYVRKDGE WVLLSTFLGR SLEVLFQGPG HHHHHHHHSA WSHPQFEKGG GSGGGGSGGS AWSHP QFEK

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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: 26 / 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

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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K
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 / Number real images: 12804 / 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

Particle selectionNumber selected: 185400
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:

8hfx

Final reconstructionNumber classes used: 3 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51163
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:

8hfx


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

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

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