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- EMDB-81218: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-81218
TitleCryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Map dataCryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Sample
  • Complex: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
    • Protein or peptide: Tundra swan ACE2
    • Protein or peptide: Spike protein S1
KeywordsCryo-EM structure / Tundra swan ACE2 / SARS-CoV-2 / RBD / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Cygnus columbianus (tundra swan)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao FG / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Authors: Gao FG / Liu S
History
DepositionJun 4, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_81218.png

Downloads & links

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Map

FileDownload / File: emd_81218.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 256 pix.
= 171.52 Å		0.67 Å/pix.
x 256 pix.
= 171.52 Å		0.67 Å/pix.
x 256 pix.
= 171.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.036409516 - 0.06830497
Average (Standard dev.)0.00016253325 (±0.0020556531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 171.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD

Fileemd_81218_half_map_1.map
AnnotationCryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD

Fileemd_81218_half_map_2.map
AnnotationCryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD

EntireName: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
Components
  • Complex: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
    • Protein or peptide: Tundra swan ACE2
    • Protein or peptide: Spike protein S1

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Supramolecule #1: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD

SupramoleculeName: Cryo-EM structure of Tundra swan ACE2 complexed with SARS-CoV-2 RBD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Tundra swan ACE2

MacromoleculeName: Tundra swan ACE2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Cygnus columbianus (tundra swan)
Molecular weightTheoretical: 69.410906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QDVTNQAQMF LAEFNVRAED ISYESSLASW NYNTNITEET ATKMNEVGAK WSAFYEEASK NASSFLLSDI QDPLIRLQIQ SLQDRGSSV LSPEKYSRLS TVLNTMSTIY STGTVCKTTE PFDCMVLEPG LDSIMAYSID YHERLWAWEA WRADVGRMMR P LYEEYVEL ...String:
QDVTNQAQMF LAEFNVRAED ISYESSLASW NYNTNITEET ATKMNEVGAK WSAFYEEASK NASSFLLSDI QDPLIRLQIQ SLQDRGSSV LSPEKYSRLS TVLNTMSTIY STGTVCKTTE PFDCMVLEPG LDSIMAYSID YHERLWAWEA WRADVGRMMR P LYEEYVEL KNEAAKLNSY ADYGDYWRAN YEADYPEEYK YSRDQLVQDV EKTFEQIKPL YQQLHAYVRH RLEQAYGSQF IS STGCLPA HLLGDMWGRF WTNLYSLTVP YPAKPNIDVT DAMVQKNWDA MKIFKAAEAF FSSIGLYNMT EGFWKNSMLT EPT DNRKVV CHPTAWDMGK NDYRIKMCTK VTMDDFLTAH HEMGHIEYDM AYSVQPFLLR DGANEGFHEA VGEIMSLSAA TPQH LKSLN LLEPTFQEDE ETEINFLLKQ ALTIVGTMPF TYMLEKWRWM VFRGEITKQE WTKRWWEMKR DIVGVVEPVP HDETY CDPA ALFHVANDYS FIRYYTRTIY QFQFHEALCK AAKHTGPLHT CDITNSTAAG GNLRGLLELG RSKPWTQALE NLTGEK YMN ATPLLHYFEP LFNWLQKNNS GRYIGWNTDW TPYS

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.894559 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGTIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVKGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGTIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVKGFNCYFP L QSYGFQPT YGVGYQPYRV VVLSFELLHA PATVCGP

UniProtKB: Spike glycoprotein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 1.67 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 112777
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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