+Open data
-Basic information
Entry | Database: PDB / ID: 7bbh | |||||||||
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Title | Structure of Coronavirus Spike from Smuggled Guangdong Pangolin | |||||||||
Components | Surface glycoprotein | |||||||||
Keywords | VIRAL PROTEIN / Coronavirus / Pangolin / Spike / Smuggled / DSP | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Wrobel, A.G. / Benton, D.J. / Rosenthal, P.B. / Gamblin, S.J. | |||||||||
Funding support | United Kingdom, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7bbh.cif.gz | 574.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bbh.ent.gz | 481.5 KB | Display | PDB format |
PDBx/mmJSON format | 7bbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bbh_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7bbh_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7bbh_validation.xml.gz | 95.9 KB | Display | |
Data in CIF | 7bbh_validation.cif.gz | 144.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bbh ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bbh | HTTPS FTP |
-Related structure data
Related structure data | 12130MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 138407.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pangolin coronavirus / Production host: Homo sapiens (human) / References: UniProt: A0A6M3G9R1 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #3: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pangolin Coronavirus Spike Ectodomain Trimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.41 MDa / Experimental value: NO |
Source (natural) | Organism: Pangolin coronavirus |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 6 |
Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 51.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Version: 2.14 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93000 / Symmetry type: POINT | ||||||||||||||||||||||||
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