+Open data
-Basic information
Entry | Database: PDB / ID: 7f7e | ||||||
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Title | SARS-CoV-2 S protein RBD in complex with A5-10 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN / Antibody / SARS-CoV-2 / VIRUS | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Dou, Y. / Wang, X. / Wang, K. / Liu, P. / Lu, B. | ||||||
Citation | Journal: Emerg Microbes Infect / Year: 2022 Title: Etesevimab in combination with JS026 neutralizing SARS-CoV-2 and its variants. Authors: Wang, F. / Li, L. / Dou, Y. / Shi, R. / Duan, X. / Liu, H. / Zhang, J. / Liu, D. / Wu, J. / He, Y. / Lan, J. / Lu, B. / Feng, H. / Yan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f7e.cif.gz | 257.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f7e.ent.gz | 207.6 KB | Display | PDB format |
PDBx/mmJSON format | 7f7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f7e_validation.pdf.gz | 477.9 KB | Display | wwPDB validaton report |
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Full document | 7f7e_full_validation.pdf.gz | 495.2 KB | Display | |
Data in XML | 7f7e_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 7f7e_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f7e ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f7e | HTTPS FTP |
-Related structure data
Related structure data | 6vsbS 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
#1: Antibody | Mass: 24014.896 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: 22182.643 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: 22246.904 Da / Num. of mol.: 1 / Fragment: RBD domain 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: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 63.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris, PEG 6000, 100mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1.071 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.071 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 30468 / % possible obs: 96.03 % / Redundancy: 9.6 % / CC1/2: 0.995 / Net I/σ(I): 14.22 |
Reflection shell | Resolution: 2.49→2.579 Å / Num. unique obs: 2375 / CC1/2: 0.565 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VSB Resolution: 2.49→20.37 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.09 / 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: 239.84 Å2 / Biso mean: 84.1721 Å2 / Biso min: 28.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→20.37 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -1.1001 Å / Origin y: -24.2536 Å / Origin z: -15.3946 Å
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Refinement TLS group |
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