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- EMDB-34730: Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-... -
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Open data
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Basic information
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Title | Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in complex with white-tailed deer ACE2 | |||||||||
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![]() | Complex / VIRAL PROTEIN | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / host cell surface receptor binding / 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 / proteolysis / extracellular space / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
![]() | Han P / Meng YM / Qi JX | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of white-tailed deer, , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity. Authors: Pu Han / Yumin Meng / Di Zhang / Zepeng Xu / Zhiyuan Li / Xiaoqian Pan / Zhennan Zhao / Linjie Li / Lingfeng Tang / Jianxun Qi / Kefang Liu / George F Gao / ![]() Abstract: SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of ...SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals. IMPORTANCE Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 169.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 43.5 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 318 MB 318 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1005.3 KB | Display | ![]() |
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Full document | ![]() | 1004.9 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hg0MC ![]() 8hfxC ![]() 8hfyC ![]() 8hfzC ![]() 8ifyC ![]() 8ifzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34730_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34730_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SARS-CoV-2 prototype spike protein receptor-binding domain in com...
Entire | Name: SARS-CoV-2 prototype spike protein receptor-binding domain in complex with white-tailed deer ACE2 |
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Components |
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-Supramolecule #1: SARS-CoV-2 prototype spike protein receptor-binding domain in com...
Supramolecule | Name: SARS-CoV-2 prototype spike protein receptor-binding domain in complex with white-tailed deer ACE2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Angiotensin-converting enzyme
Macromolecule | Name: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 71.420438 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MTGSFWLLLS LVAVTAAQST TEEQAKTFLE KFNHEAEDLS YQSSLASWNY NTNITDENVQ KMNEARAKWS AFYEEQSRMA KTYSLEEIQ NLTLKRQLKA LQQSGTSVLS AEKSKRLNTI LNTMSTIYST GKVLDPNTQE CLALEPGLDD IMENSRDYNR R LWAWEGWR ...String: MTGSFWLLLS LVAVTAAQST TEEQAKTFLE KFNHEAEDLS YQSSLASWNY NTNITDENVQ KMNEARAKWS AFYEEQSRMA KTYSLEEIQ NLTLKRQLKA LQQSGTSVLS AEKSKRLNTI LNTMSTIYST GKVLDPNTQE CLALEPGLDD IMENSRDYNR R LWAWEGWR AEVGKQLRPL YEEYVVLENE MARANNYEDY GDYWRGDYEV TEAGDYDYSR DQLMKDVENT FAEIKPLYEQ LH AYVRAKL MDTYPSYISP TGCLPAHLLG DMWGRFWTNL YSLTVPFKHK PSIDVTEKMK NQSWDAERIF KEAEKFFVSI SLP HMTQGF WDNSMLTEPG DGRKVVCHPT AWDLGKGDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAA QPYLLRDGAN EGFH EAVGE IMSLSAATPH YLKALGLLEP DFYEDNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFKG EIPKEQWMEK WWEMK REIV GVVEPLPHDE TYCDPACLFH VAEDYSFIRY YTRTIYQFQF HEALCKTANH EGALFKCDIS NSTEAGQRLL QMLSLG KSE PWTLALESIV GIKTMDVKPL LNYFEPLFTW LKEQNRNSFV GWSTEWTPYS UniProtKB: Angiotensin-converting enzyme |
-Macromolecule #2: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.873496 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGP UniProtKB: Spike glycoprotein |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |