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- PDB-3x0g: Crystal structure of the ectodomain of African green monkey CD81 ... -
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Open data
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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) | ||||||
![]() | CD81 | ||||||
![]() | CELL ADHESION / disulfide bond / helical bundle / immune cell adhesion / morphology / activation / proliferation / differentiation / Membrane | ||||||
Function / homology | ![]() : / 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 / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Zhang, M. / Cui, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.4 KB | Display | ![]() |
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PDB format | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436 KB | Display | ![]() |
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Full document | ![]() | 438.4 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3x0eC ![]() 3x0fC ![]() 4bkh C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() | ||||
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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