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Yorodumi- PDB-7x9e: Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x9e | ||||||
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Title | Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / SARS-CoV-2 / Antibody / Fab / Spike / Fusion peptide / 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 / membrane fusion / 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: 2.6 Å | ||||||
Authors | Chen, X. / Zhang, T. / Ding, J. / Sun, X. / Sun, B. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2022 Title: Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2. Authors: Sun, X. / Yi, C. / Zhu, Y. / Ding, L. / Xia, S. / Chen, X. / Liu, M. / Gu, C. / Lu, X. / Fu, Y. / Chen, S. / Zhang, T. / Zhang, Y. / Yang, Z. / Ma, L. / Gu, W. / Hu, G. / Du, S. / Yan, R. / ...Authors: Sun, X. / Yi, C. / Zhu, Y. / Ding, L. / Xia, S. / Chen, X. / Liu, M. / Gu, C. / Lu, X. / Fu, Y. / Chen, S. / Zhang, T. / Zhang, Y. / Yang, Z. / Ma, L. / Gu, W. / Hu, G. / Du, S. / Yan, R. / Fu, W. / Yuan, S. / Qiu, C. / Zhao, C. / Zhang, X. / He, Y. / Qu, A. / Zhou, X. / Li, X. / Wong, G. / Deng, Q. / Zhou, Q. / Lu, H. / Ling, Z. / Ding, J. / Lu, L. / Xu, J. / Xie, Y. / Sun, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x9e.cif.gz | 338.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x9e.ent.gz | 275.2 KB | Display | PDB format |
PDBx/mmJSON format | 7x9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x9e_validation.pdf.gz | 472.1 KB | Display | wwPDB validaton report |
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Full document | 7x9e_full_validation.pdf.gz | 483 KB | Display | |
Data in XML | 7x9e_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 7x9e_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/7x9e ftp://data.pdbj.org/pub/pdb/validation_reports/x9/7x9e | HTTPS FTP |
-Related structure data
Related structure data | 6bqbS S: Starting model for refinement |
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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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23378.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 22949.475 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: Abvec-HIgG1 / Production host: Cricetulus griseus (Chinese hamster) #3: Protein/peptide | Mass: 2785.198 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC2 #4: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1M sodium citrate pH 4.5, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2021 |
Radiation | Monochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 30037 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2953 / CC1/2: 0.534 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BQB Resolution: 2.6→38.88 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.82 / 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: 87.79 Å2 / Biso mean: 34.683 Å2 / Biso min: 13.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→38.88 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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