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- EMDB-38793: The structure of fox ACE2 and Omicron BF.7 RBD complex -

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Basic information

Entry
Database: EMDB / ID: EMD-38793
TitleThe structure of fox ACE2 and Omicron BF.7 RBD complex
Map data
Sample
  • Complex: The structure of fox ACE2 and PT RBD complex
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: ZINC ION
Keywordsfox ACE2 / VIRAL PROTEIN / Omicron BF.7
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / brush border membrane / cilium / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / brush border membrane / cilium / metallopeptidase activity / virus receptor activity / Maturation of spike protein / endopeptidase activity / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Vulpes vulpes (red fox)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
Authorssun JQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82225021 China
CitationJournal: Virol Sin / Year: 2024
Title: The binding and structural basis of fox ACE2 to RBDs from different sarbecoviruses.
Authors: Junsen Chen / Junqing Sun / Zepeng Xu / Linjie Li / Xinrui Kang / Chunliang Luo / Qi Wang / Xueyang Guo / Yan Li / Kefang Liu / Ying Wu /
Abstract: Foxes are susceptible to SARS-CoV-2 in laboratory settings, and there have also been reports of natural infections of both SARS-CoV and SARS-CoV-2 in foxes. In this study, we assessed the binding ...Foxes are susceptible to SARS-CoV-2 in laboratory settings, and there have also been reports of natural infections of both SARS-CoV and SARS-CoV-2 in foxes. In this study, we assessed the binding capacities of fox ACE2 to important sarbecoviruses, including SARS-CoV, SARS-CoV-2, and animal-origin SARS-CoV-2 related viruses. Our findings demonstrated that fox ACE2 exhibits broad binding capabilities to receptor-binding domains (RBDs) of sarbecoviruses. We further determined the cryo-EM structures of fox ACE2 complexed with RBDs of SARS-CoV, SARS-CoV-2 prototype (PT), and Omicron BF.7. Through structural analysis, we identified that the K417 mutation can weaken the ability of SARS-CoV-2 sub-variants to bind to fox ACE2, thereby reducing the susceptibility of foxes to SARS-CoV-2 sub-variants. In addition, the Y498 residue in the SARS-CoV RBD plays a crucial role in forming a vital cation-π interaction with K353 in the fox ACE2 receptor. This interaction is the primary determinant for the higher affinity of the SARS-CoV RBD compared to that of the SARS-CoV-2 PT RBD. These results indicate that foxes serve as potential hosts for numerous sarbecoviruses, highlighting the critical importance of surveillance efforts.
History
DepositionJan 21, 2024-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38793.png

Downloads & links

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Map

FileDownload / File: emd_38793.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.69 Å
Density
Contour LevelBy AUTHOR: 0.123
Minimum - Maximum-0.0017788792 - 1.6748574
Average (Standard dev.)0.0033647136 (±0.042873293)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 176.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38793_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_38793_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 : The structure of fox ACE2 and PT RBD complex

EntireName: The structure of fox ACE2 and PT RBD complex
Components
  • Complex: The structure of fox ACE2 and PT RBD complex
    • Protein or peptide: Spike protein S1
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: ZINC ION

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Supramolecule #1: The structure of fox ACE2 and PT RBD complex

SupramoleculeName: The structure of fox ACE2 and PT RBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron/BF.7
Molecular weightTheoretical: 27.899781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHSSALLCCL VLLTGVRARV QPTESIVRFP NITNLCPFDE VFNATTFASV YAWNRKRISN CVADYSVLYN FAPFFAFKCY GVSPTKLND LCFTNVYADS FVIRGNEVSQ IAPGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKVGGNY NYRYRLFRKS N LKPFERDI ...String:
MHSSALLCCL VLLTGVRARV QPTESIVRFP NITNLCPFDE VFNATTFASV YAWNRKRISN CVADYSVLYN FAPFFAFKCY GVSPTKLND LCFTNVYADS FVIRGNEVSQ IAPGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKVGGNY NYRYRLFRKS N LKPFERDI STEIYQAGNK PCNGVAGVNC YFPLQSYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VN FHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Vulpes vulpes (red fox)
Molecular weightTheoretical: 71.030781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSGSSWLLLS LAALTAAQST EDLVNTFLEK FNYEAEELSY QSSLASWDYN TNISDENVQK MNNAGAKWSA FYEEQSKLAK TYPLEEIQD STVKRQLRAL QHSGSSVLSA DKNQRLNTIL NSMSTIYSTG KACNPSNPQE CLLLEPGLDD IMENSKDYNE R LWAWEGWR ...String:
MSGSSWLLLS LAALTAAQST EDLVNTFLEK FNYEAEELSY QSSLASWDYN TNISDENVQK MNNAGAKWSA FYEEQSKLAK TYPLEEIQD STVKRQLRAL QHSGSSVLSA DKNQRLNTIL NSMSTIYSTG KACNPSNPQE CLLLEPGLDD IMENSKDYNE R LWAWEGWR SEVGKQLRPL YEEYVALKNE MARANNYEDY GDYWRGDYEE EWENGYNYSR NQLIDDVEHT FTQIMPLYQH LH AYVRTKL MDTYPSYISP TGCLPAHLLG DMWGRFWTNL YPLTVPFGQK PNIDVTNAMV NQSWDARKIF KEAEKFFVSV GLP NMTQGF WENSMLTEPS DSRKVVCHPT AWDLGKGDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAA QPFLLRNGAN EGFH EAVGE IMSLSAATPN HLKNIGLLPP SFFEDSETEI NFLLKQALTI VGTLPFTYML EKWRWMVFKG EIPKDQWMKT WWEMK RNIV GVVEPVPHDE TYCDPASLFH VANDYSFIRY YTRTIYQFQF QEALCQIAKH EGPLHKCDIS NSSEAGQKLL EMLKLG KSK PWTYALEIVV GAKNMDVRPL LNYFEPLFTW LKEQNRNSFV GWNTDWSPYA

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.01 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69826
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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