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Yorodumi- EMDB-12130: Structure of Coronavirus Spike from Smuggled Guangdong Pangolin -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12130 | |||||||||
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Title | Structure of Coronavirus Spike from Smuggled Guangdong Pangolin | |||||||||
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: 2.9 Å | |||||||||
Authors | Wrobel AG / Benton DJ / Rosenthal PB / Gamblin SJ | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2. Authors: Antoni G Wrobel / Donald J Benton / Pengqi Xu / Lesley J Calder / Annabel Borg / Chloë Roustan / Stephen R Martin / Peter B Rosenthal / John J Skehel / Steven J Gamblin / Abstract: Coronaviruses of bats and pangolins have been implicated in the origin and evolution of the pandemic SARS-CoV-2. We show that spikes from Guangdong Pangolin-CoVs, closely related to SARS-CoV-2, bind ...Coronaviruses of bats and pangolins have been implicated in the origin and evolution of the pandemic SARS-CoV-2. We show that spikes from Guangdong Pangolin-CoVs, closely related to SARS-CoV-2, bind strongly to human and pangolin ACE2 receptors. We also report the cryo-EM structure of a Pangolin-CoV spike protein and show it adopts a fully-closed conformation and that, aside from the Receptor-Binding Domain, it resembles the spike of a bat coronavirus RaTG13 more than that of SARS-CoV-2. | |||||||||
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_12130.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-12130-v30.xml emd-12130.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12130_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_12130.png | 172.6 KB | ||
Masks | emd_12130_msk_1.map | 244.1 MB | Mask map | |
Others | emd_12130_half_map_1.map.gz emd_12130_half_map_2.map.gz | 226.8 MB 226.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12130 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12130 | HTTPS FTP |
-Validation report
Summary document | emd_12130_validation.pdf.gz | 413.5 KB | Display | EMDB validaton report |
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Full document | emd_12130_full_validation.pdf.gz | 412.6 KB | Display | |
Data in XML | emd_12130_validation.xml.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12130 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12130 | HTTPS FTP |
-Related structure data
Related structure data | 7bbhMC 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_12130.map.gz / Format: CCP4 / Size: 244.1 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: 1.078 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12130_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12130_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12130_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pangolin Coronavirus Spike Ectodomain Trimer
Entire | Name: Pangolin Coronavirus Spike Ectodomain Trimer |
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Components |
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-Supramolecule #1: Pangolin Coronavirus Spike Ectodomain Trimer
Supramolecule | Name: Pangolin Coronavirus Spike Ectodomain Trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Pangolin coronavirus |
Recombinant expression | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 410 KDa |
-Macromolecule #1: Surface glycoprotein
Macromolecule | Name: Surface 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: 138.407031 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MLFFFFLHFA LVNSQCVNLT GRAAIQPSFT NSSQRGVYYP DTIFRSNTLV LSQGYFLPFY SNVSWYYALT KTNSAEKRVD NPVLDFKDG IYFAATEKSN IVRGWIFGTT LDNTSQSLLI VNNATNVIIK VCNFQFCYDP YLSGYYHNNK TWSTREFAVY S SYANCTFE ...String: MLFFFFLHFA LVNSQCVNLT GRAAIQPSFT NSSQRGVYYP DTIFRSNTLV LSQGYFLPFY SNVSWYYALT KTNSAEKRVD NPVLDFKDG IYFAATEKSN IVRGWIFGTT LDNTSQSLLI VNNATNVIIK VCNFQFCYDP YLSGYYHNNK TWSTREFAVY S SYANCTFE YVSKSFMLDI AGKSGLFDTL REFVFRNVDG YFKIYSKYTP VNVNSNLPIG FSALEPLVEI PAGINITKFR TL LTIHRGD PMPNNGWTVF SAAYYVGYLA PRTFMLNYNE NGTITDAVDC ALDPLSEAKC TLKSLTVEKG IYQTSNFRVQ PTE SIVRFP NITNLCPFGE VFNATTFASV YAWNRKRISN CVADYSVLYN STSFSTFKCY GVSPTKLNDL CFTNVYADSF VVRG DEVRQ IAPGQTGRIA DYNYKLPDDF TGCVIAWNSN NLDSKVGGNY NYLYRLFRKS NLKPFERDIS TEIYQAGSTP CNGVE GFNC YFPLQSYGFH PTNGVGYQPY RVVVLSFELL KAPATVCGPK QSTNLVKNKC VNFNFNGLTG TGVLTESSKK FLPFQQ FGR DIADTTDAVR DPQTLEILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQDVNC TEVPVAIHAD QLTPTWRVYS TGSNVFQ TR AGCLIGAEHV NNTYECDIPI GAGICASYQT NTNSRSVSSQ AIIAYTMSLG AENSVAYANN SIAIPTNFTI SVTTEILP V SMTKTSVDCT MYICGDSIEC SNLLLQYGSF CTQLNRALTG IAVEQDKNTQ EVFAQVKQIY KTPPIKDFGG FNFSQILPD PSKPSKRSFI EDLLFNKVTL ADAGFIKQYG DCLGDIAARD LICAQKFNGL TVLPPLLTDE MIAQYTSALL AGTITSGWTF GAGAALQIP FAMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LSSTASALGK LQDVVNQNAQ ALNTLVKQLS S NFGAISSV LNDILSRLDP PEAEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YH LMSFPQS APHGVVFLHV TYVPSQEKNF TTTPAICHEG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGS CDV VIGIVN NTVYDPLQPE LDSFKEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQ SGREN LYFQGGGGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGHHH HHH |
-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: 45 / 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
Concentration | 0.15 mg/mL |
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Buffer | pH: 6 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
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) / Detector mode: COUNTING / Average electron dose: 51.8 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 |