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Yorodumi- PDB-6w41: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w41 | |||||||||
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Title | Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Antibody / Virus / Complex / SARS-CoV-2 / 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.084 Å | |||||||||
Authors | Yuan, M. / Wu, N.C. / Zhu, X.Y. / Wilson, I.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2020 Title: A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Authors: Yuan, M. / Wu, N.C. / Zhu, X. / Lee, C.D. / So, R.T.Y. / Lv, H. / Mok, C.K.P. / 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 | 6w41.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w41.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 6w41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w41_validation.pdf.gz | 474 KB | Display | wwPDB validaton report |
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Full document | 6w41_full_validation.pdf.gz | 477.9 KB | Display | |
Data in XML | 6w41_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 6w41_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/6w41 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/6w41 | HTTPS FTP |
-Related structure data
Related structure data | 2ajfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 23455.420 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: 24376.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 2 molecules C
#3: Protein | Mass: 26095.348 Da / Num. of mol.: 1 / Fragment: receptor binding domain 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 |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 3 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical |
-Details
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: 7.37 Å3/Da / Density % sol: 83.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 80 mM sodium acetate pH 4.6, 1.5 M ammonium sulfate, and 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.08→50.039 Å / Num. obs: 41184 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.142 / Χ2: 0.777 / Net I/σ(I): 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AJF Resolution: 3.084→50.039 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 204.71 Å2 / Biso mean: 99.0524 Å2 / Biso min: 45.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.084→50.039 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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