+Open data
-Basic information
Entry | Database: PDB / ID: 5m4r | ||||||||||||
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Title | Structural tuning of CD81LEL (space group C2) | ||||||||||||
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: 3.1 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. #1: Journal: EMBO J. / Year: 2001 Title: CD81 extracellular domain 3D structure: insight into the tetraspanin superfamily structural motifs. Authors: Kitadokoro, K. / Bordo, D. / Galli, G. / Petracca, R. / Falugi, F. / Abrignani, S. / Grandi, G. / Bolognesi, M. #2: Journal: Biol. Chem. / Year: 2002 Title: Subunit association and conformational flexibility in the head subdomain of human CD81 large extracellular loop. Authors: Kitadokoro, K. / Ponassi, M. / Galli, G. / Petracca, R. / Falugi, F. / Grandi, G. / Bolognesi, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m4r.cif.gz | 249.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m4r.ent.gz | 210.2 KB | Display | PDB format |
PDBx/mmJSON format | 5m4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m4r_validation.pdf.gz | 483.6 KB | Display | wwPDB validaton report |
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Full document | 5m4r_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 5m4r_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5m4r_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/5m4r ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m4r | HTTPS FTP |
-Related structure data
Related structure data | 5m2cC 5m33C 5m3dC 5m3tC 1g8qS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 11182.417 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: in chain E the last residue has been modelled as ALA Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Plasmid: pHLSec / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60033 #2: Chemical | #3: Chemical | |
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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: 3.85 Å3/Da / Density % sol: 68.1 % Description: small (about 40x60x15 microns) brick-like morphology weak diffractor but reasonable to 3.1 Ang |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Protein: ~10mg/ml Buffer: 0.1 M NaCitrate pH 4.0, 0.8 M (NH4)2 SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→53.1 Å / Num. obs: 15510 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2 / CC1/2: 0.817 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G8Q Resolution: 3.1→53.093 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 31.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→53.093 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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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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