+Open data
-Basic information
Entry | Database: PDB / ID: 5m2c | ||||||||||||
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Title | Structural tuning of CD81LEL (space group P32 1 2) | ||||||||||||
Components | CD81 antigen | ||||||||||||
Keywords | CELL ADHESION / human cellular receptor for Hepatitis C virus | ||||||||||||
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 / transferrin receptor binding / immunological synapse formation / protein localization to lysosome / positive regulation of T-helper 2 cell cytokine production / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / humoral immune response mediated by circulating immunoglobulin / MHC class II protein binding / 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 / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / MHC class II protein complex binding / virus receptor activity / 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: 1.961 Å | ||||||||||||
Authors | Cunha, E.S. / Sfriso, P. / Rojas, A.L. / Roversi, P. / Hospital, A. / Orozco, M. / Abrescia, N.G. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Structure / Year: 2017 Title: Mechanism of Structural Tuning of the Hepatitis C Virus Human Cellular Receptor CD81 Large Extracellular Loop. Authors: Cunha, E.S. / Sfriso, P. / Rojas, A.L. / Roversi, P. / Hospital, A. / Orozco, M. / Abrescia, N.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m2c.cif.gz | 110.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m2c.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m2c_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 5m2c_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 5m2c_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 5m2c_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m2/5m2c ftp://data.pdbj.org/pub/pdb/validation_reports/m2/5m2c | HTTPS FTP |
-Related structure data
Related structure data | 5m33C 5m3dC 5m3tC 5m4rC 1g8qS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11182.417 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: large-extracellular-loop / Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Plasmid: pHLSec / Cell (production host): human embryo kidney / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60033 #2: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 29% EtOH, 0.092 M Citrate pH 2.2, 0.113 M Na2HPO4 pH 9.3, (pH ~5) 39% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→41.1 Å / Num. obs: 13921 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 50.4 |
Reflection shell | Resolution: 1.96→2.02 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.866 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G8Q Resolution: 1.961→41.067 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.6
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.961→41.067 Å
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Refine LS restraints |
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LS refinement shell |
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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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