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Yorodumi- PDB-6xc2: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xc2 | ||||||||||||
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Title | Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1 | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Antibody / SARS-CoV-2 / Coronavirus / Spike / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||||||||
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 / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 | Severe acute respiratory syndrome coronavirus 2 Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.112 Å | ||||||||||||
Authors | Yuan, M. / Liu, H. / Wu, N.C. / Zhu, X. / Wilson, I.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Science / Year: 2020 Title: Structural basis of a shared antibody response to SARS-CoV-2. Authors: Yuan, M. / Liu, H. / Wu, N.C. / Lee, C.D. / Zhu, X. / Zhao, F. / Huang, D. / Yu, W. / Hua, Y. / Tien, H. / Rogers, T.F. / Landais, E. / Sok, D. / Jardine, J.G. / Burton, D.R. / Wilson, I.A. #1: Journal: Biorxiv / Year: 2020 Title: Structural basis of a public antibody response to SARS-CoV-2. Authors: Yuan, M. / Liu, H. / Wu, N.C. / Lee, C.D. / Zhu, X. / Zhao, F. / Huang, D. / Yu, W. / Hua, Y. / Tien, H. / Rogers, T.F. / Landais, E. / Sok, D. / Jardine, J.G. / Burton, D.R. / Wilson, I.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xc2.cif.gz | 250.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xc2.ent.gz | 197.6 KB | Display | PDB format |
PDBx/mmJSON format | 6xc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xc2_validation.pdf.gz | 494.1 KB | Display | wwPDB validaton report |
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Full document | 6xc2_full_validation.pdf.gz | 511.8 KB | Display | |
Data in XML | 6xc2_validation.xml.gz | 44 KB | Display | |
Data in CIF | 6xc2_validation.cif.gz | 59.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/6xc2 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/6xc2 | HTTPS FTP |
-Related structure data
Related structure data | 6xc3C 6xc4C 6xc7C 4zd3S 6ylaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 26095.348 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: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2 #2: Antibody | Mass: 23641.365 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) #3: Antibody | Mass: 23150.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) #4: Sugar | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium citrate pH 5.5 15% polyethylene glycol 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.11→50 Å / Num. obs: 25802 / % possible obs: 88.3 % / Redundancy: 1.5 % / CC1/2: 0.97 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.2→3.27 Å / Num. unique obs: 1234 / CC1/2: 0.62 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZD3, 6YLA Resolution: 3.112→40.343 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.44 / Stereochemistry target values: ML
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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 max: 140.13 Å2 / Biso mean: 70 Å2 / Biso min: 31.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.112→40.343 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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