+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38784 | |||||||||
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Title | The structure of fox ACE2 and PT RBD complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | fox ACE2/PT RBD / VIRAL PROTEIN | |||||||||
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 / endopeptidase activity / Maturation of spike protein / 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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Vulpes vulpes (red fox) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | sun JQ | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38784.map.gz | 56.5 MB | EMDB map data format | |
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Header (meta data) | emd-38784-v30.xml emd-38784.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_38784.png | 27.1 KB | ||
Filedesc metadata | emd-38784.cif.gz | 5.9 KB | ||
Others | emd_38784_half_map_1.map.gz emd_38784_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38784 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38784 | HTTPS FTP |
-Validation report
Summary document | emd_38784_validation.pdf.gz | 688.6 KB | Display | EMDB validaton report |
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Full document | emd_38784_full_validation.pdf.gz | 688.1 KB | Display | |
Data in XML | emd_38784_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_38784_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38784 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38784 | HTTPS FTP |
-Related structure data
Related structure data | 8xyzMC 8xzbC 8xzdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38784.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.69 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38784_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38784_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The structure of fox ACE2 and PT RBD complex
Entire | Name: The structure of fox ACE2 and PT RBD complex |
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Components |
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-Supramolecule #1: The structure of fox ACE2 and PT RBD complex
Supramolecule | Name: The structure of fox ACE2 and PT RBD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Signal peptide, Spike protein S1
Macromolecule | Name: Signal peptide, Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 30.635682 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSCVLLFPTA PGQRAGYCAV SSFWQRIRHH VCVSCASSSC VITMQSATTE SIVRFPNITN LCPFGEVFNA TRFASVYAWN RKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYNY KLPDDFTGCV I AWNSNNLD ...String: MSCVLLFPTA PGQRAGYCAV SSFWQRIRHH VCVSCASSSC VITMQSATTE SIVRFPNITN LCPFGEVFNA TRFASVYAWN RKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYNY KLPDDFTGCV I AWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL QSYGFQPTNG VGYQPYRVVV LS FELLHAP ATVCGPKKST NLVKNKCVNF HHHHHH UniProtKB: Spike glycoprotein |
-Macromolecule #2: Angiotensin-converting enzyme
Macromolecule | Name: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: Vulpes vulpes (red fox) |
Molecular weight | Theoretical: 71.030781 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 217439 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |