+Open data
-Basic information
Entry | Database: PDB / ID: 5tcx | |||||||||
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Title | Crystal structure of human tetraspanin CD81 | |||||||||
Components | CD81 antigen | |||||||||
Keywords | CELL INVASION / tetraspanin / transmembrane / cholesterol | |||||||||
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 / cholesterol binding / positive regulation of T cell receptor signaling pathway / 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 Complement cascade / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / 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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å | |||||||||
Authors | Zimmerman, B. / McMillan, B.J. / Seegar, T.C.M. / Kruse, A.C. / Blacklow, S.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2016 Title: Crystal Structure of a Full-Length Human Tetraspanin Reveals a Cholesterol-Binding Pocket. Authors: Zimmerman, B. / Kelly, B. / McMillan, B.J. / Seegar, T.C. / Dror, R.O. / Kruse, A.C. / Blacklow, S.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tcx.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tcx.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 5tcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/5tcx ftp://data.pdbj.org/pub/pdb/validation_reports/tc/5tcx | HTTPS FTP |
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-Related structure data
Related structure data | 1g8qS 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: 27203.586 Da / Num. of mol.: 1 / Mutation: C6S, C9S, C227S, C228S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60033 |
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#2: Chemical | ChemComp-CLR / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.81 % |
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Crystal grow | Temperature: 291 K / Method: lipidic cubic phase / pH: 8 / Details: 25-35% PEG300, Ammonium citrate dibasic, Tris / PH range: 7.6-8.2 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→36.755 Å / Num. obs: 5006 / % possible obs: 98.6 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.18 / Net I/av σ(I): 5.9 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.95→3.03 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.3 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G8Q Resolution: 2.955→36.755 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.955→36.755 Å
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Refine LS restraints |
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LS refinement shell |
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