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- PDB-5m33: Structural tuning of CD81LEL (space group P21) -

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Basic information

Entry
Database: PDB / ID: 5m33
TitleStructural tuning of CD81LEL (space group P21)
ComponentsCD81 antigen
KeywordsCELL ADHESION / human cellular receptor for Hepatitis C virus / signaling protein
Function / homology
Function and homology information


positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / macrophage fusion / CD4-positive, alpha-beta T cell costimulation / positive regulation of B cell receptor signaling pathway / osteoclast fusion / myoblast fusion involved in skeletal muscle regeneration / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of inflammatory response to antigenic stimulus / regulation of macrophage migration ...positive regulation of adaptive immune memory response / positive regulation of protein catabolic process in the vacuole / macrophage fusion / CD4-positive, alpha-beta T cell costimulation / positive regulation of B cell receptor signaling pathway / osteoclast fusion / myoblast fusion involved in skeletal muscle regeneration / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of inflammatory response to antigenic stimulus / regulation of macrophage migration / immunological synapse formation / transferrin receptor binding / tetraspanin-enriched microdomain / positive regulation of protein exit from endoplasmic reticulum / protein localization to lysosome / positive regulation of T-helper 2 cell cytokine production / 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 receptor clustering / positive regulation of B cell proliferation / basal plasma membrane / Regulation of Complement cascade / protein localization to plasma membrane / regulation of protein stability / receptor internalization / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / cytosol
Similarity search - Function
Cd81 Antigen, Extracellular Domain; Chain: A / Tetraspanin / Tetraspanin, conserved site / Transmembrane 4 family signature. / Tetraspanin, animals / Tetraspanin, EC2 domain superfamily / Tetraspanin/Peripherin / Tetraspanin family / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsCunha, E.S. / Sfriso, P. / Rojas, A.L. / Roversi, P. / Hospital, A. / Orozco, M. / Abrescia, N.G.
Funding support Spain, 3items
OrganizationGrant numberCountry
MINECOBIO2012-32868 Spain
MINECOBFU2012-33947 Spain
MINECOBFU2015-64541-R Spain
CitationJournal: 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
DepositionOct 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD81 antigen
B: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7999
Polymers22,3652
Non-polymers4347
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-4 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.445, 75.846, 37.363
Angle α, β, γ (deg.)90.00, 107.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CD81 antigen / 26 kDa cell surface protein TAPA-1 / Target of the antiproliferative antibody 1 / Tetraspanin-28 / Tspan-28


Mass: 11182.417 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.4 % / Description: excellent diffractor - rodlike shape
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 10 mg/ml Buffer: 0.1 M MIB pH 5.0, 25% w/v PEG 1500 grown in presence of synthetic claudin-I long-extracellular-loop (CLDN1-EL1) - but not visible in electron density. cryo- ...Details: Protein: 10 mg/ml Buffer: 0.1 M MIB pH 5.0, 25% w/v PEG 1500 grown in presence of synthetic claudin-I long-extracellular-loop (CLDN1-EL1) - but not visible in electron density. cryo-protectant: 25% glycerol + peptide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972499 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972499 Å / Relative weight: 1
ReflectionResolution: 1.28→26 Å / Num. obs: 38224 / % possible obs: 88.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 21.6
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.934 / % possible all: 40.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8Q

1g8q


Resolution: 1.28→25.997 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.02
RfactorNum. reflection% reflection
Rfree0.1729 1911 5.01 %
Rwork0.1363 --
obs0.1382 38175 88.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.28→25.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1361 0 28 194 1583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011484
X-RAY DIFFRACTIONf_angle_d1.182001
X-RAY DIFFRACTIONf_dihedral_angle_d13.727553
X-RAY DIFFRACTIONf_chiral_restr0.07237
X-RAY DIFFRACTIONf_plane_restr0.006263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2785-1.31050.2619560.20171195X-RAY DIFFRACTION40
1.3105-1.34590.224870.16611612X-RAY DIFFRACTION55
1.3459-1.38550.1771170.1462045X-RAY DIFFRACTION70
1.3855-1.43030.17731440.13992454X-RAY DIFFRACTION84
1.4303-1.48140.16831500.12732774X-RAY DIFFRACTION96
1.4814-1.54070.17481430.12022930X-RAY DIFFRACTION99
1.5407-1.61080.17051390.11672887X-RAY DIFFRACTION99
1.6108-1.69570.16231550.11842884X-RAY DIFFRACTION99
1.6957-1.80190.15141620.1262916X-RAY DIFFRACTION99
1.8019-1.9410.16511500.13662897X-RAY DIFFRACTION99
1.941-2.13630.18481480.13142910X-RAY DIFFRACTION99
2.1363-2.44520.15821500.12722938X-RAY DIFFRACTION99
2.4452-3.07990.16351530.14552901X-RAY DIFFRACTION98
3.0799-26.00260.18311570.14192921X-RAY DIFFRACTION98

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