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Yorodumi- PDB-6ejg: CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ejg | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CD81 LARGE EXTRACELLULAR LOOP IN COMPLEX WITH SINGLE CHAIN FV FRAGMENT 4 | ||||||
Components |
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Keywords | CELL ADHESION / HELICAL BUNDLE / ANTIBODY-ANTIGEN COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / CD4-positive, alpha-beta T cell costimulation / osteoclast fusion / positive regulation of B cell receptor signaling pathway / myoblast fusion involved in skeletal muscle regeneration / positive regulation of inflammatory response to antigenic stimulus / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of macrophage migration / macrophage fusion / immunological synapse formation / transferrin receptor binding / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / MHC class II protein binding / humoral immune response mediated by circulating immunoglobulin / positive regulation of CD4-positive, alpha-beta T cell proliferation / cellular response to low-density lipoprotein particle stimulus / cholesterol binding / positive regulation of T cell receptor signaling pathway / immunological synapse / basal plasma membrane / positive regulation of B cell proliferation / positive regulation of receptor clustering / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / virus receptor activity / MHC class II protein complex binding / basolateral plasma membrane / vesicle / positive regulation of MAPK cascade / focal adhesion / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å | ||||||
Authors | Harris, S.F. / Wong, A. / Kuglstatter, A. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structure-Guided Combinatorial Engineering Facilitates Affinity and Specificity Optimization of Anti-CD81 Antibodies. Authors: Nelson, B. / Adams, J. / Kuglstatter, A. / Li, Z. / Harris, S.F. / Liu, Y. / Bohini, S. / Ma, H. / Klumpp, K. / Gao, J. / Sidhu, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ejg.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ejg.ent.gz | 104.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ejg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ejg_validation.pdf.gz | 451.8 KB | Display | wwPDB validaton report |
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Full document | 6ejg_full_validation.pdf.gz | 462.3 KB | Display | |
Data in XML | 6ejg_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 6ejg_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6ejg ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6ejg | HTTPS FTP |
-Related 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: 10922.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Production host: Escherichia coli (E. coli) / References: UniProt: P60033 #2: Antibody | Mass: 26399.332 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #3: 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: 4.19 Å3/Da / Density % sol: 70.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM sodium citrate, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→46.83 Å / Num. obs: 27051 / % possible obs: 88.3 % / Redundancy: 6.3 % / Rsym value: 0.17 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.82→2.92 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1126 / Rsym value: 0.494 / % possible all: 37.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→46.83 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.873 / SU B: 12.326 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.346 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.385 Å2
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Refinement step | Cycle: 1 / Resolution: 2.82→46.83 Å
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