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- PDB-4g8e: Crystal Structure of clone18 TCR -

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Basic information

Entry
Database: PDB / ID: 4g8e
TitleCrystal Structure of clone18 TCR
Components
  • alpha chain clone 18 TCR
  • beta chain clone 18 TCR
KeywordsIMMUNE SYSTEM / TCR / T cell / CD1b / GMM / lipid recognition
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / immune response / membrane / plasma membrane
Similarity search - Function
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / T cell receptor beta constant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsGras, S. / Bhati, M. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2013
Title: A conserved human T cell population targets mycobacterial antigens presented by CD1b.
Authors: Van Rhijn, I. / Kasmar, A. / de Jong, A. / Gras, S. / Bhati, M. / Doorenspleet, M.E. / de Vries, N. / Godfrey, D.I. / Altman, J.D. / de Jager, W. / Rossjohn, J. / Moody, D.B.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha chain clone 18 TCR
B: beta chain clone 18 TCR


Theoretical massNumber of molelcules
Total (without water)50,1212
Polymers50,1212
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-24 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.420, 84.090, 58.280
Angle α, β, γ (deg.)90.000, 111.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha chain clone 18 TCR


Mass: 22298.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#2: Protein beta chain clone 18 TCR


Mass: 27822.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG1500, 10% Proprionate-cacodylate-bis tris propane pH 7, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 36.271 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.40.2355.4913678420886.8
2.4-2.50.177.686858185599.7
2.5-2.60.1359.625901159199.3
2.6-2.70.11311.750611376100
2.7-30.07216.4211409308799.5
3-40.0427.5516463467196.5
4-50.02936.096175172299.3
5-60.02935.39274377598.2
6-100.02536.77294983099.4
100.02241.1881523395.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NW2

2nw2


Resolution: 2.2→45.48 Å / Cor.coef. Fo:Fc: 0.9045 / Cor.coef. Fo:Fc free: 0.8549 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 1059 5.13 %RANDOM
Rwork0.2412 ---
obs0.2439 20660 97.62 %-
Displacement parametersBiso max: 111.8 Å2 / Biso mean: 37.089 Å2 / Biso min: 3.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.3673 Å20 Å2-0.2248 Å2
2---5.0619 Å20 Å2
3---6.4291 Å2
Refine analyzeLuzzati coordinate error obs: 0.614 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 0 146 3625
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1205SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes515HARMONIC5
X-RAY DIFFRACTIONt_it3564HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion454SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3962SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3564HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4836HARMONIC21.4
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion23.28
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.5685 141 5.1 %
Rwork0.4768 2621 -
all0.481 2762 -
obs--97.62 %

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