[English] 日本語
Yorodumi- PDB-7a5r: Complex of SARS-CoV-2 spike and CR3022 Fab (Non-Uniform Refinement) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a5r | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Complex of SARS-CoV-2 spike and CR3022 Fab (Non-Uniform Refinement) | ||||||||||||
Components |
| ||||||||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / Antibody | ||||||||||||
Function / homology | Function and homology information 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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Wrobel, A.G. / Benton, D.J. / Rosenthal, P.B. / Gamblin, S.J. | ||||||||||||
Funding support | United Kingdom, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Antibody-mediated disruption of the SARS-CoV-2 spike glycoprotein. Authors: Antoni G Wrobel / Donald J Benton / Saira Hussain / Ruth Harvey / Stephen R Martin / Chloë Roustan / Peter B Rosenthal / John J Skehel / Steven J Gamblin / Abstract: The CR3022 antibody, selected from a group of SARS-CoV monoclonal antibodies for its ability to cross-react with SARS-CoV-2, has been examined for its ability to bind to the ectodomain of the SARS- ...The CR3022 antibody, selected from a group of SARS-CoV monoclonal antibodies for its ability to cross-react with SARS-CoV-2, has been examined for its ability to bind to the ectodomain of the SARS-CoV-2 spike glycoprotein. Using cryo-electron microscopy we show that antibody binding requires rearrangements in the S1 domain that result in dissociation of the spike. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7a5r.cif.gz | 283.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7a5r.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 7a5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a5r_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7a5r_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7a5r_validation.xml.gz | 55.6 KB | Display | |
Data in CIF | 7a5r_validation.cif.gz | 80.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/7a5r ftp://data.pdbj.org/pub/pdb/validation_reports/a5/7a5r | HTTPS FTP |
-Related structure data
Related structure data | 11648MC 7a5sC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Antibody | Mass: 27408.861 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 26511.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 142271.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #4: Polysaccharide | Source method: isolated from a genetically manipulated source Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of SARS-CoV-2 Spike trimer with CR3022 Fab fragment Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo heidelbergensis (Heidelberg man) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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: 33.6 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: EPU / Version: 2.7 / Category: image acquisition |
---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88000 / Symmetry type: POINT |
Atomic model building | PDB-ID: 6W41 |