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Yorodumi- PDB-7e8m: Crystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e8m | ||||||
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Title | Crystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 spike / receptor binding domain / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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: 2.09 Å | ||||||
Authors | Wang, X.Q. / Zhang, L.Q. / Ge, J.W. / Wang, R.K. / Lan, J. | ||||||
Citation | Journal: Immunity / Year: 2021 Title: Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species. Authors: Wang, R. / Zhang, Q. / Ge, J. / Ren, W. / Zhang, R. / Lan, J. / Ju, B. / Su, B. / Yu, F. / Chen, P. / Liao, H. / Feng, Y. / Li, X. / Shi, X. / Zhang, Z. / Zhang, F. / Ding, Q. / Zhang, T. / Wang, X. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e8m.cif.gz | 260.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e8m.ent.gz | 206.1 KB | Display | PDB format |
PDBx/mmJSON format | 7e8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e8m_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 7e8m_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 7e8m_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 7e8m_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/7e8m ftp://data.pdbj.org/pub/pdb/validation_reports/e8/7e8m | HTTPS FTP |
-Related structure data
Related structure data | 7cdiS 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: Protein | Mass: 21907.557 Da / Num. of mol.: 1 / Mutation: K417N, E484K, N501Y 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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#2: Antibody | Mass: 22851.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 23274.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 12%w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→26.17 Å / Num. obs: 50710 / % possible obs: 90.92 % / Redundancy: 5.3 % / CC1/2: 0.997 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.09→2.17 Å / Num. unique obs: 3033 / CC1/2: 0.762 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CDI Resolution: 2.09→26.17 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.85 / 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: 110.55 Å2 / Biso mean: 41.7495 Å2 / Biso min: 20.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→26.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Origin x: -59.8228 Å / Origin y: 3.8823 Å / Origin z: 26.8046 Å
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Refinement TLS group |
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