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Yorodumi- PDB-3x0g: Crystal structure of the ectodomain of African green monkey CD81 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3x0g | ||||||
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Title | Crystal structure of the ectodomain of African green monkey CD81 large extracellular loop (agmCD81-LEL) | ||||||
Components | CD81 | ||||||
Keywords | CELL ADHESION / disulfide bond / helical bundle / immune cell adhesion / morphology / activation / proliferation / differentiation / Membrane | ||||||
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 ...: / 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 / transferrin receptor binding / immunological synapse formation / 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 / cholesterol binding / positive regulation of T cell receptor signaling pathway / plasma membrane => GO:0005886 / cellular response to low-density lipoprotein particle stimulus / immunological synapse / positive regulation of B cell proliferation / positive regulation of receptor clustering / basal plasma membrane / protein localization to plasma membrane / regulation of protein stability / receptor internalization / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / virus receptor activity / positive regulation of transcription by RNA polymerase II / extracellular exosome Similarity search - Function | ||||||
Biological species | Chlorocebus sabaeus (green monkey) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 Å | ||||||
Authors | Zhang, M. / Cui, S. | ||||||
Citation | Journal: Faseb J. / Year: 2015 Title: An intramolecular bond at cluster of differentiation 81 ectodomain is important for hepatitis C virus entry. Authors: Yang, W. / Zhang, M. / Chi, X. / Liu, X. / Qin, B. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x0g.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x0g.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 3x0g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3x0g_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 3x0g_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 3x0g_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 3x0g_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/3x0g ftp://data.pdbj.org/pub/pdb/validation_reports/x0/3x0g | HTTPS FTP |
-Related structure data
Related structure data | 3x0eC 3x0fC 4bkh C: citing same article (ref.) 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: 10204.521 Da / Num. of mol.: 1 / Fragment: large extracellular loop Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorocebus sabaeus (green monkey) / Gene: CD81 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A0D9RBI8*PLUS | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 5% Ethanol, 5% MPD, 0.1M Tris pH 8.5, 200mM Sodium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 27, 2014 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.899→27.878 Å / Num. all: 7800 / Num. obs: 7580 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.93 % / Biso Wilson estimate: 31.196 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.28 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 2.52 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.42 / Num. unique all: 1219 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BKH 4bkh Resolution: 1.899→25.276 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.585 Å2 / ksol: 0.327 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.899→25.276 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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