[English] 日本語
Yorodumi
- EMDB-72208: Cryo EM structure of elk ACE2 in complex with XBB 1.5 spike RBD -

+
Open data


ID or keywords:

Loading...

-
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: 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, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72208.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_72208_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72208_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72208_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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)

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
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

+
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more