+Open data
-Basic information
Entry | Database: PDB / ID: 7xnf | ||||||
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Title | Structure of SARS-CoV-2 antibody P2C-1F11 with GX/P2V/2017 RBD | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / GX/P2V/2017 / RBD / antibody / P2C1-F11 / Fab | ||||||
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 | Homo sapiens (human) Pangolin coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Jia, Y.F. / Chai, Y. / Wang, Q.H. / Gao, G.F. | ||||||
Funding support | 1items
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Citation | Journal: Cell Rep / Year: 2022 Title: Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017. Authors: Jia, Y. / Niu, S. / Hu, Y. / Chai, Y. / Zheng, A. / Su, C. / Wu, L. / Han, P. / Han, P. / Lu, D. / Liu, Z. / Yan, X. / Tian, D. / Chen, Z. / Qi, J. / Tian, W.X. / Wang, Q. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xnf.cif.gz | 137.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xnf.ent.gz | 95.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xnf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xnf_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 7xnf_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 7xnf_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 7xnf_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/7xnf ftp://data.pdbj.org/pub/pdb/validation_reports/xn/7xnf | HTTPS FTP |
-Related structure data
Related structure data | 7xswC 7cdiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23983.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23361.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Protein | Mass: 24237.365 Da / Num. of mol.: 1 / Fragment: BetaCoV S1-CTD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pangolin coronavirus / Production host: Homo sapiens (human) / References: UniProt: A0A6G6A2Q2 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M MES monohydrate (pH 6.0), 20% w/v Polyethylene glycol monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→50 Å / Num. obs: 22549 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 48.31 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 11.905 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.925 / Num. unique obs: 2186 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CDI Resolution: 2.79→41.61 Å / SU ML: 0.6908 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.7352 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→41.61 Å
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Refine LS restraints |
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LS refinement shell |
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