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- PDB-5m4r: Structural tuning of CD81LEL (space group C2) -

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Basic information

Entry
Database: PDB / ID: 5m4r
TitleStructural tuning of CD81LEL (space group C2)
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 19, 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
E: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,38611
Polymers55,9125
Non-polymers4746
Water00
1
A: CD81 antigen
D: CD81 antigen


Theoretical massNumber of molelcules
Total (without water)22,3652
Polymers22,3652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-16 kcal/mol
Surface area9090 Å2
MethodPISA
2
B: CD81 antigen
E: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6816
Polymers22,3652
Non-polymers3164
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-33 kcal/mol
Surface area9120 Å2
MethodPISA
3
C: CD81 antigen
hetero molecules

C: CD81 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6816
Polymers22,3652
Non-polymers3164
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2250 Å2
ΔGint-51 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.120, 104.970, 65.010
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
211chain B and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
311chain D and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
411chain C and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)
511chain E and (resseq 115:136 or resseq 143:160 or resseq 188:200 ) and (not element H)

NCS ensembles :
ID
1
2
3
4
5

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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.: 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 ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
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: 3.85 Å3/Da / Density % sol: 68.1 %
Description: small (about 40x60x15 microns) brick-like morphology weak diffractor but reasonable to 3.1 Ang
Crystal growTemperature: 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

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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: 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 shellResolution: 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

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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: 3.1→53.093 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 31.61
RfactorNum. reflection% reflection
Rfree0.2459 762 4.98 %
Rwork0.2256 --
obs0.2267 15306 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→53.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 27 0 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073358
X-RAY DIFFRACTIONf_angle_d0.9584514
X-RAY DIFFRACTIONf_dihedral_angle_d12.3741207
X-RAY DIFFRACTIONf_chiral_restr0.031541
X-RAY DIFFRACTIONf_plane_restr0.003585
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A413X-RAY DIFFRACTIONPOSITIONAL
12B413X-RAY DIFFRACTIONPOSITIONAL0.025
13D413X-RAY DIFFRACTIONPOSITIONAL0.063
14C413X-RAY DIFFRACTIONPOSITIONAL0.06
15E413X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.33930.28541370.26312746X-RAY DIFFRACTION93
3.3393-3.67530.28391430.26872949X-RAY DIFFRACTION99
3.6753-4.2070.25531530.232939X-RAY DIFFRACTION99
4.207-5.29960.24021560.21042961X-RAY DIFFRACTION99
5.2996-53.10060.2281730.21092949X-RAY DIFFRACTION97
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)
16.5144-0.6294-0.3549.39240.12737.63390.1640.26790.3772-0.4783-0.16480.3351-0.3418-0.3612-0.04660.9196-0.04350.02780.7545-0.02140.539717.2093-7.63223.3515
21.92710.0855-0.25774.62242.70794.2390.08030.11060.5230.52650.7361-1.1052-1.73711.6101-0.67591.1203-0.25030.15850.9487-0.11810.960929.0082-7.509316.6151
37.24162.16711.12676.8339-0.55157.023-0.28390.2201-0.6235-0.62160.26930.0162-0.14270.4454-0.01450.7585-0.06830.04610.5172-0.03810.645234.50298.1534-10.7304
42.74161.3655-0.31745.59981.964.49360.371-0.5070.25940.9585-0.42880.07620.8212-0.46480.09650.7262-0.13810.04190.60470.0120.609833.61-0.5041-0.0717
58.7134-0.2133-0.35921.45251.1586.79230.293-0.0595-0.4597-0.1860.1088-0.5498-0.35370.1915-0.42850.5142-0.0379-0.01290.39260.0230.48347.6481-16.6356-1.0368
64.32293.40551.97452.88020.3224.7838-0.20430.11170.63330.08530.16181.1865-2.0014-0.7025-0.14880.93630.1301-0.04340.61180.05820.640916.8076-6.33730.9551
77.47910.30831.25418.21441.32819.84750.4037-0.178-0.46851.0932-0.37120.67340.962-1.40020.03880.8201-0.10660.06460.8360.00480.63114.5711-13.45337.7119
81.63621.0141.08865.12192.14582.63860.62770.0238-0.11920.1025-0.1939-0.84220.23030.4902-0.30961.1816-0.00360.08170.70250.07330.740422.265-14.328949.1799
96.27921.66460.45756.51840.63616.87550.33090.37430.4107-1.3962-0.3306-0.0475-0.6245-0.4990.07190.98520.04320.06920.61830.00680.672333.516923.0963-10.3706
101.48391.063-1.24245.25560.57914.3310.3788-0.9537-0.15251.1921-0.07210.9030.56930.04950.42840.9968-0.07820.16380.6244-0.0690.782234.629632.655-0.6687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 115:157 or resid 189:200)
2X-RAY DIFFRACTION2chain A and (resid 158:188)
3X-RAY DIFFRACTION3chain B and (resid 114:157 or resid 189:200)
4X-RAY DIFFRACTION4chain B and (resid 158:188)
5X-RAY DIFFRACTION5chain C and (resid 114:157 or resid 189:200)
6X-RAY DIFFRACTION6chain C and (resid 158:188)
7X-RAY DIFFRACTION7chain D and (resid 114:157 or resid 189:201)
8X-RAY DIFFRACTION8chain D and (resid 158:188)
9X-RAY DIFFRACTION9chain E and (resid 114:157 or resid 189:203)
10X-RAY DIFFRACTION10chain E and (resid 158:188)

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