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- PDB-5m3d: Structural tuning of CD81LEL (space group P31) -

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Basic information

Entry
Database: PDB / ID: 5m3d
TitleStructural tuning of CD81LEL (space group P31)
ComponentsCD81 antigen
KeywordsCELL 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 / 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 / positive regulation of T-helper 2 cell cytokine production / protein localization to lysosome / 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 / immunological synapse / cellular response to low-density lipoprotein particle stimulus / 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
PHOSPHATE ION / CD81 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 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 1.4Nov 20, 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
C: CD81 antigen
D: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,67216
Polymers44,7304
Non-polymers94212
Water18010
1
A: CD81 antigen
D: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8038
Polymers22,3652
Non-polymers4386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-9 kcal/mol
Surface area8690 Å2
MethodPISA
2
B: CD81 antigen
C: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8698
Polymers22,3652
Non-polymers5046
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-27 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.948, 97.948, 34.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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.: 4 / Fragment: UNP residues 112-201
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.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: Protein: 10 mg/ml Buffer: 40% EtOH, 0.097 M Citrate pH 2.2, 0.113 M Na2HPO4 pH 9.3, (pH ~6) 2.5% PEG 1000
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.38→48.97 Å / Num. obs: 14545 / % possible obs: 98.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.034 / Net I/σ(I): 12.3
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.676 / % possible all: 98.9

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Processing

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

1g8q


Resolution: 2.38→48.974 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 740 5.09 %
Rwork0.1738 --
obs0.1763 14539 98.12 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→48.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 54 10 2794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092810
X-RAY DIFFRACTIONf_angle_d1.0093773
X-RAY DIFFRACTIONf_dihedral_angle_d14.7371005
X-RAY DIFFRACTIONf_chiral_restr0.036442
X-RAY DIFFRACTIONf_plane_restr0.004489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3801-2.56390.28951460.2352779X-RAY DIFFRACTION99
2.5639-2.82190.26481560.1942793X-RAY DIFFRACTION99
2.8219-3.23010.25471390.19092782X-RAY DIFFRACTION99
3.2301-4.06930.20791640.16282738X-RAY DIFFRACTION98
4.0693-48.98430.2061350.16362707X-RAY DIFFRACTION96
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)
16.7332-2.36760.05087.4793-1.68655.54030.04340.2340.4144-0.4586-0.3078-0.9503-0.09180.62880.23950.59590.09320.02730.49450.08950.6228-22.9456-21.08924.1491
25.52920.5987-1.22993.7022-1.93723.4252-0.4684-0.7745-1.06980.1258-0.1079-0.30080.65330.08330.56470.71390.13390.0890.62230.19130.6973-25.5098-32.894210.9578
39.06030.57610.85775.95520.19266.5206-0.18450.62240.9159-0.1268-0.3069-0.0525-0.54650.32560.43960.3232-0.0199-0.0640.51710.06870.50056.8504-30.3073-7.2844
44.77770.33270.29022.9545-2.49074.5977-0.0572-0.5891-0.07350.2083-0.7031-0.69490.25730.81470.56430.5074-0.011-0.11350.73350.15680.653215.7333-38.5764-0.5159
57.18860.23921.01056.1499-0.17175.47940.0150.42840.6121-0.3264-0.1896-0.0217-0.1538-0.00680.27960.3910.1169-0.08930.65010.0140.5192-6.4606-33.081-13.2174
63.42251.42320.98084.3894-0.89094.01160.0846-0.578-0.44620.0814-0.46860.82380.6795-0.33440.290.63120.0692-0.09960.7207-0.1040.8526-16.6337-41.9077-9.3696
76.5627-1.59390.1057.0008-0.00815.7007-0.14220.31150.2562-0.57560.0207-0.5069-0.130.18790.160.66230.0131-0.02620.38190.07960.5349-31.9047-10.9892-1.7281
85.9927-0.77520.43913.5831-0.66534.8902-0.4602-0.49470.13380.21250.04350.5862-0.0166-0.52770.35630.66220.0111-0.13610.4958-0.00180.7157-44.5872-6.55032.0753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 113:157 or resid 189:202)
2X-RAY DIFFRACTION2chain A and (resid 158:188)
3X-RAY DIFFRACTION3chain B and (resid 113:157 or resid 189:202)
4X-RAY DIFFRACTION4chain B and (resid 158:188)
5X-RAY DIFFRACTION5chain C and (resid 114:157 or resid 189:202)
6X-RAY DIFFRACTION6chain C and (resid 158:188)
7X-RAY DIFFRACTION7chain D and (resid 114:157 or resid 189:202)
8X-RAY DIFFRACTION8chain D and (resid 158:188)

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