+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32693 | |||||||||
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Title | Structure of PDF-2180-COV RBD binding to Bat37 ACE2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | merbecovirus / PDF-2180-CoV / RBD / ACE2 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / endocytosis involved in viral entry into host cell / cilium / metallopeptidase activity / receptor-mediated virion attachment to host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / endocytosis involved in viral entry into host cell / cilium / metallopeptidase activity / receptor-mediated virion attachment to host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular space / membrane / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bat coronavirus / Pipistrellus pipistrellus (common pipistrelle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Cao L / Wang X / Tortorici MA / Veesler D | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2022 Title: Close relatives of MERS-CoV in bats use ACE2 as their functional receptors. Authors: Qing Xiong / Lei Cao / Chengbao Ma / M Alejandra Tortorici / Chen Liu / Junyu Si / Peng Liu / Mengxue Gu / Alexandra C Walls / Chunli Wang / Lulu Shi / Fei Tong / Meiling Huang / Jing Li / ...Authors: Qing Xiong / Lei Cao / Chengbao Ma / M Alejandra Tortorici / Chen Liu / Junyu Si / Peng Liu / Mengxue Gu / Alexandra C Walls / Chunli Wang / Lulu Shi / Fei Tong / Meiling Huang / Jing Li / Chufeng Zhao / Chao Shen / Yu Chen / Huabin Zhao / Ke Lan / Davide Corti / David Veesler / Xiangxi Wang / Huan Yan / Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) and several bat coronaviruses use dipeptidyl peptidase-4 (DPP4) as an entry receptor. However, the receptor for NeoCoV-the closest known MERS- ...Middle East respiratory syndrome coronavirus (MERS-CoV) and several bat coronaviruses use dipeptidyl peptidase-4 (DPP4) as an entry receptor. However, the receptor for NeoCoV-the closest known MERS-CoV relative found in bats-remains unclear. Here, using a pseudotype virus entry assay, we found that NeoCoV and its close relative, PDF-2180, can efficiently bind to and use specific bat angiotensin-converting enzyme 2 (ACE2) orthologues and, less favourably, human ACE2 as entry receptors through their receptor-binding domains (RBDs) on the spike (S) proteins. Cryo-electron microscopy analysis revealed an RBD-ACE2 binding interface involving protein-glycan interactions, distinct from those of other known ACE2-using coronaviruses. We identified residues 337-342 of human ACE2 as a molecular determinant restricting NeoCoV entry, whereas a NeoCoV S pseudotyped virus containing a T510F RBD mutation efficiently entered cells expressing human ACE2. Although polyclonal SARS-CoV-2 antibodies or MERS-CoV RBD-specific nanobodies did not cross-neutralize NeoCoV or PDF-2180, an ACE2-specific antibody and two broadly neutralizing betacoronavirus antibodies efficiently inhibited these two pseudotyped viruses. We describe MERS-CoV-related viruses that use ACE2 as an entry receptor, underscoring a promiscuity of receptor use and a potential zoonotic threat. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32693.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-32693-v30.xml emd-32693.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_32693.png | 94.3 KB | ||
Filedesc metadata | emd-32693.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32693 | HTTPS FTP |
-Validation report
Summary document | emd_32693_validation.pdf.gz | 398.8 KB | Display | EMDB validaton report |
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Full document | emd_32693_full_validation.pdf.gz | 398.4 KB | Display | |
Data in XML | emd_32693_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_32693_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32693 | HTTPS FTP |
-Related structure data
Related structure data | 7wpzMC 7u6rC 7wpoC 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_32693.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : PDF-2180-COV RBD-Bat37 ACE2 complex
Entire | Name: PDF-2180-COV RBD-Bat37 ACE2 complex |
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Components |
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-Supramolecule #1: PDF-2180-COV RBD-Bat37 ACE2 complex
Supramolecule | Name: PDF-2180-COV RBD-Bat37 ACE2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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Source (natural) | Organism: Bat coronavirus |
-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: Pipistrellus pipistrellus (common pipistrelle) |
Molecular weight | Theoretical: 69.511125 KDa |
Recombinant expression | Organism: Homo (humans) |
Sequence | String: TTEEEARDFL DKFNSEAENL SHESALASWD YNTNITDENA QKMNEADSKW SDFYKEQSKR AQAFPLQEIQ NLTIKLQLQI LQQNGSSVL TAEKSKRLST ILTTMSTIYS TGKVCNPNNP QQCFTLSGLE DIMEKSKDYH QRLWVWEGWR SEVGKQLRPL Y EEYVVLKN ...String: TTEEEARDFL DKFNSEAENL SHESALASWD YNTNITDENA QKMNEADSKW SDFYKEQSKR AQAFPLQEIQ NLTIKLQLQI LQQNGSSVL TAEKSKRLST ILTTMSTIYS TGKVCNPNNP QQCFTLSGLE DIMEKSKDYH QRLWVWEGWR SEVGKQLRPL Y EEYVVLKN EMARGNNYED YGDYWRGDYE TEGEDGYNYS RNQLMEDVDR IFLEIKPLYE QLHAYVRAKL MNAYPSRISP TG CLPAHLL GDMWGRFWTN LYNLTVPFEQ KQNIDVTETM KKQSWDAEKI FKEAEKFYLS VGLYSMTQGF WNNSMLTEPS DGR QVVCHP TAWDLGEDDF RIKMCTKVTM DDFLTAHHEM GHIQYDMAYA KQPYLLRNGA NEGFHEAVGE VMSLSVATPK HLKG MGLLP SDFSEDNETE INFLLKQALN IVGTLPFTYM LEKWRWMVFE GKIPKEQWME KWWEMKREIV GVVEPLPHDE TYCDP ASLF HVANDYSFIR YFTRTILEFQ FQEALCKIAK HEGPLHKCDI SNSTEAGKKL KDMLELGKSK PWTYALNQIA RTKEMD AKP LLNYFEPLFS WLKKQNGNSV GWSADWSPYS EQ UniProtKB: Angiotensin-converting enzyme |
-Macromolecule #2: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bat coronavirus |
Molecular weight | Theoretical: 22.960801 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: AHVYPDCNFT DLFRENAPTI MQYKRQVFTR CNYNLTLLLS LVQVDEFVCD KITPEALATG CYSSLTVDWF AFPYAWKSYL AIGSADRIV RFNYNQDYSN PSCRIHSKVN SSVGISYSGL YSYITNCNYG GFNKDDVVKP GGRASQPCVT GALNSPTNGQ V WSFNFGGV ...String: AHVYPDCNFT DLFRENAPTI MQYKRQVFTR CNYNLTLLLS LVQVDEFVCD KITPEALATG CYSSLTVDWF AFPYAWKSYL AIGSADRIV RFNYNQDYSN PSCRIHSKVN SSVGISYSGL YSYITNCNYG GFNKDDVVKP GGRASQPCVT GALNSPTNGQ V WSFNFGGV PYRTSRLTYT DHLKNPLDMV YVITVKYEPG AETVCP UniProtKB: Spike glycoprotein |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k 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: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130308 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |