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- PDB-4g8f: Crystal Structure of clone42 TCR -

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Basic information

Entry
Database: PDB / ID: 4g8f
TitleCrystal Structure of clone42 TCR
Components
  • alpha chain clone 42 TCR
  • beta chain clone 42 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding ...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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / immune response / extracellular exosome / 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 / Immunoglobulins / Immunoglobulin-like fold ...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: 2.1 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 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software / Item: _reflns_shell.percent_possible_all / _software.name
Revision 1.4Sep 13, 2023Group: 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

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Assembly

Deposited unit
A: alpha chain clone 42 TCR
B: beta chain clone 42 TCR


Theoretical massNumber of molelcules
Total (without water)49,9592
Polymers49,9592
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-22 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.520, 56.790, 85.890
Angle α, β, γ (deg.)90.000, 101.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha chain clone 42 TCR


Mass: 22646.074 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 42 TCR


Mass: 27312.568 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.: 231 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%PEG3350, 0.05m Na-HEPES pH 7, 1% tryptone, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.1→84.19 Å / Num. obs: 25774 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.525 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.30.4872.823063607999.7
2.3-2.40.3134.4288242332100
2.4-2.50.2445.67545198399.8
2.5-2.60.1877.146483171599.8
2.6-2.70.1498.8654681449100
2.7-30.09712.7712333326699.6
3-40.04523.919200513099.9
4-50.03233.726729184199.5
5-60.03233.59297682999.8
6-100.02934.35328789399.7
100.02238.4188925797.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.10.0refinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2nw2

2nw2


Resolution: 2.1→33.73 Å / Cor.coef. Fo:Fc: 0.9366 / Cor.coef. Fo:Fc free: 0.9171 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 1313 5.1 %RANDOM
Rwork0.2026 ---
obs0.2044 25764 99.82 %-
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 41.517 Å2 / Biso min: 19.81 Å2
Baniso -1Baniso -2Baniso -3
1-5.6043 Å20 Å2-3.3247 Å2
2---4.841 Å20 Å2
3----0.7634 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å
Refinement stepCycle: LAST / Resolution: 2.1→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 231 3597
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1197SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes514HARMONIC5
X-RAY DIFFRACTIONt_it3512HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
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_contact3966SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3512HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4772HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion22.16
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2456 133 4.64 %
Rwork0.2282 2733 -
all0.229 2866 -
obs--99.82 %

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