+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30418 | |||||||||
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Title | Cryo-EM structure of PCoV_GX spike glycoprotein | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | |||||||||
Biological species | Pangolin coronavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | |||||||||
Authors | Wang X / Yu J / Zhang S / Qiao S / Zeng J / Tian L | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution. Authors: Shuyuan Zhang / Shuyuan Qiao / Jinfang Yu / Jianwei Zeng / Sisi Shan / Long Tian / Jun Lan / Linqi Zhang / Xinquan Wang / Abstract: In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species ...In recognizing the host cellular receptor and mediating fusion of virus and cell membranes, the spike (S) glycoprotein of coronaviruses is the most critical viral protein for cross-species transmission and infection. Here we determined the cryo-EM structures of the spikes from bat (RaTG13) and pangolin (PCoV_GX) coronaviruses, which are closely related to SARS-CoV-2. All three receptor-binding domains (RBDs) of these two spike trimers are in the "down" conformation, indicating they are more prone to adopt the receptor-binding inactive state. However, we found that the PCoV_GX, but not the RaTG13, spike is comparable to the SARS-CoV-2 spike in binding the human ACE2 receptor and supporting pseudovirus cell entry. We further identified critical residues in the RBD underlying different activities of the RaTG13 and PCoV_GX/SARS-CoV-2 spikes. These results collectively indicate that tight RBD-ACE2 binding and efficient RBD conformational sampling are required for the evolution of SARS-CoV-2 to gain highly efficient infection. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30418.map.gz | 6.8 MB | EMDB map data format | |
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Header (meta data) | emd-30418-v30.xml emd-30418.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30418_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_30418.png | 84.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30418 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30418 | HTTPS FTP |
-Validation report
Summary document | emd_30418_validation.pdf.gz | 372.3 KB | Display | EMDB validaton report |
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Full document | emd_30418_full_validation.pdf.gz | 371.9 KB | Display | |
Data in XML | emd_30418_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_30418_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30418 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30418 | HTTPS FTP |
-Related structure data
Related structure data | 7cn8MC 7cn4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30418.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : PCoV_GX glycoprotein
Entire | Name: PCoV_GX glycoprotein |
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Components |
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-Supramolecule #1: PCoV_GX glycoprotein
Supramolecule | Name: PCoV_GX glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Pangolin coronavirus |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Glycoprotein
Macromolecule | Name: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Pangolin coronavirus |
Molecular weight | Theoretical: 143.501922 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MFVFLFVLPL VSSQCVNLTT RTGIPPGYTN SSTRGVYYPD KVFRSSILHL TQDLFLPFFS NVTWFNTINY QGGFKKFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD ARTQSLLIVN NATNVVIKVC EFQFCTDPFL GVYYHNNNKT WVENEFRVYS S ANNCTFEY ...String: MFVFLFVLPL VSSQCVNLTT RTGIPPGYTN SSTRGVYYPD KVFRSSILHL TQDLFLPFFS NVTWFNTINY QGGFKKFDNP VLPFNDGVY FASTEKSNII RGWIFGTTLD ARTQSLLIVN NATNVVIKVC EFQFCTDPFL GVYYHNNNKT WVENEFRVYS S ANNCTFEY ISQPFLMDLE GKQGNFKNLR EFVFKNVDGY FKIYSKHTPI DLVRDLPRGF AALEPLVDLP IGINITRFQT LL ALHRSYL TPGNLESGWT TGAAAYYVGY LQQRTFLLSY NQNGTITDAV DCSLDPLSET KCTLKSLTVE KGIYQTSNFR VQP TISIVR FPNITNLCPF GEVFNASKFA SVYAWNRKRI SNCVADYSVL YNSTSFSTFK CYGVSPTKLN DLCFTNVYAD SFVV KGDEV RQIAPGQTGV IADYNYKLPD DFTGCVIAWN SVKQDALTGG NYGYLYRLFR KSKLKPFERD ISTEIYQAGS TPCNG QVGL NCYYPLERYG FHPTTGVNYQ PFRVVVLSFE LLNGPATVCG PKLSTTLVKD KCVNFNFNGL TGTGVLTTSK KQFLPF QQF GRDISDTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQDV NCTEVPMAIH AEQLTPAWRV YSAGANV FQ TRAGCLVGAE HVNNSYECDI PVGAGICASY HSMSSLRSVN QRSIIAYTMS LGAENSVAYS NNSIAIPTNF TISVTTEI L PVSMTKTSVD CTMYICGDSI ECSNLLLQYG SFCTQLNRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKDF GGFNFSQIL PDPSKPSKRS FIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQ IPFAMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALNTLVKQ L SSNFGAIS SVLNDILSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KG YHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPAICH EGKAHFPREG VFVSNGTHWF ITQRNFYEPQ IITTDNTFVS GSC DVVIGI VNNTVYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESPIDLQE LGKY EQYIK GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE KGSDYKDDDD K |
-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: 27 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #4: LINOLEIC ACID
Macromolecule | Name: LINOLEIC ACID / type: ligand / ID: 4 / Number of copies: 3 / Formula: EIC |
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Molecular weight | Theoretical: 280.445 Da |
Chemical component information | ChemComp-EIC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.2 |
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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |