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- PDB-5m3t: Structural tuning of CD81LEL (space group P64) -

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Basic information

Entry
Database: PDB / ID: 5m3t
TitleStructural tuning of CD81LEL (space group P64)
ComponentsCD81 antigen
KeywordsIMMUNE SYSTEM / 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 / 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 / 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
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: 2.021 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
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
DepositionOct 17, 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

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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)22,84411
Polymers22,3652
Non-polymers4799
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-26 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.300, 101.300, 35.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

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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 / Fragment: LEL domain, UNP residues 112-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD81, TAPA1, TSPAN28 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60033
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 10 mg/ml Buffer: 0.1 MMT pH 5, 25% w/v PEG 1500 grown in presence of fexofenadine although not visible in the electron density map

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.02→50.65 Å / Num. obs: 12501 / % possible obs: 88.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 29.1
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.802 / % possible all: 53.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8Q

1g8q


Resolution: 2.021→50.65 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 26.76
RfactorNum. reflection% reflection
Rfree0.2084 601 4.81 %
Rwork0.1717 --
obs0.1735 12489 88.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.021→50.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1384 0 27 19 1430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061421
X-RAY DIFFRACTIONf_angle_d0.8281900
X-RAY DIFFRACTIONf_dihedral_angle_d10.575513
X-RAY DIFFRACTIONf_chiral_restr0.032225
X-RAY DIFFRACTIONf_plane_restr0.003247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0207-2.2240.27981110.21392096X-RAY DIFFRACTION63
2.224-2.54580.22421540.19463060X-RAY DIFFRACTION92
2.5458-3.20740.25931700.20883316X-RAY DIFFRACTION100
3.2074-50.66590.18361660.15293416X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.4681.9936-1.15259.5039-1.54426.71630.4485-0.4986-0.24350.7549-0.42540.13690.02860.0840.01020.5107-0.10150.01380.26770.03460.3023-35.916915.8326-1.5404
21.90830.5366-0.41942.69731.22832.32880.25880.3654-0.1137-0.8923-0.09620.4644-0.1536-0.5668-0.00040.69330.033-0.06170.49280.0390.5444-42.57558.9726-10.1825
35.53050.9228-1.10079.0393-1.39175.02250.5351-0.47340.03411.0472-0.6462-0.4717-0.01180.43610.00720.5635-0.1841-0.04790.36710.01750.3492-25.746325.6715-4.4068
41.48750.3339-1.11072.4043-1.83571.85750.13620.3870.0876-0.0994-0.15920.46730.0468-0.2260.00060.4898-0.08250.04980.3855-0.02030.4628-25.7435.2324-14.8029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resid 114 : 155) or (resid 191:202))
2X-RAY DIFFRACTION2chain 'A' and (resid 156:190)
3X-RAY DIFFRACTION3chain 'B' and ((resid 112:155) or (resid 191:202))
4X-RAY DIFFRACTION4chain 'B' and (resid 156:190)

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