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- PDB-6at6: Crystal structure of the KFJ5 TCR -

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Basic information

Entry
Database: PDB / ID: 6at6
TitleCrystal structure of the KFJ5 TCR
Components
  • T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera
  • T-cell receptor beta variable 28, Human nkt tcr beta chain chimera
KeywordsIMMUNE SYSTEM / Immunogolbulin
Function / homology
Function and homology information


T cell receptor complex / response to bacterium / peptide antigen binding / adaptive immune response / cell surface receptor signaling pathway / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 variable 4 / T cell receptor beta variable 28 / Human nkt tcr beta chain / T-cell receptor, sp3.4 alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.417 Å
AuthorsGully, B.S. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2018
Title: Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide.
Authors: Chan, K.F. / Gully, B.S. / Gras, S. / Beringer, D.X. / Kjer-Nielsen, L. / Cebon, J. / McCluskey, J. / Chen, W. / Rossjohn, J.
History
DepositionAug 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: T-cell receptor beta variable 28, Human nkt tcr beta chain chimera
A: T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera


Theoretical massNumber of molelcules
Total (without water)51,5552
Polymers51,5552
Non-polymers00
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-24 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.904, 73.360, 123.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein T-cell receptor beta variable 28, Human nkt tcr beta chain chimera / V_segment translation product


Mass: 28225.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV3S1, TRBV28, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B6, UniProt: K7N5M4
#2: Protein T-cell receptor alpha variable 4, T-cell receptor, sp3.4 alpha chain chimera / T-cell receptor / sp3.4 beta chain


Mass: 23329.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J268, UniProt: K7N5N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5 and 25 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.417→46.25 Å / Num. obs: 86034 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Net I/σ(I): 15.1
Reflection shellResolution: 1.417→1.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 12212 / Rpim(I) all: 0.198 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.417→39.121 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.73
RfactorNum. reflection% reflection
Rfree0.2184 4245 4.95 %
Rwork0.1975 --
obs0.1985 85838 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.417→39.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 0 618 4058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073535
X-RAY DIFFRACTIONf_angle_d1.0964788
X-RAY DIFFRACTIONf_dihedral_angle_d14.3931302
X-RAY DIFFRACTIONf_chiral_restr0.047516
X-RAY DIFFRACTIONf_plane_restr0.005625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4172-1.43330.32381210.32652498X-RAY DIFFRACTION91
1.4333-1.45010.25271460.24712648X-RAY DIFFRACTION99
1.4501-1.46780.37651300.30422752X-RAY DIFFRACTION100
1.4678-1.48640.29881560.25512654X-RAY DIFFRACTION100
1.4864-1.5060.28991320.25812727X-RAY DIFFRACTION100
1.506-1.52660.24281450.2112680X-RAY DIFFRACTION100
1.5266-1.54840.22221450.19832712X-RAY DIFFRACTION100
1.5484-1.57150.20761320.19162709X-RAY DIFFRACTION100
1.5715-1.59610.20311700.18292696X-RAY DIFFRACTION100
1.5961-1.62220.21811510.18832674X-RAY DIFFRACTION100
1.6222-1.65020.2191440.18772743X-RAY DIFFRACTION100
1.6502-1.68020.24531330.19092703X-RAY DIFFRACTION100
1.6802-1.71250.20061440.18712721X-RAY DIFFRACTION100
1.7125-1.74750.2061370.18272746X-RAY DIFFRACTION100
1.7475-1.78550.20691390.18972730X-RAY DIFFRACTION100
1.7855-1.8270.24051480.19592684X-RAY DIFFRACTION100
1.827-1.87270.2471320.19762741X-RAY DIFFRACTION100
1.8727-1.92330.22981270.22812748X-RAY DIFFRACTION100
1.9233-1.97990.25991410.24052652X-RAY DIFFRACTION97
1.9799-2.04380.19111400.19112694X-RAY DIFFRACTION99
2.0438-2.11690.19461450.17742735X-RAY DIFFRACTION100
2.1169-2.20160.23891480.18732744X-RAY DIFFRACTION100
2.2016-2.30180.27521330.23862757X-RAY DIFFRACTION100
2.3018-2.42320.21991520.2052732X-RAY DIFFRACTION100
2.4232-2.5750.21691530.19222742X-RAY DIFFRACTION100
2.575-2.77370.21551430.19962801X-RAY DIFFRACTION100
2.7737-3.05280.2161330.18682773X-RAY DIFFRACTION100
3.0528-3.49430.19151370.17292802X-RAY DIFFRACTION100
3.4943-4.40140.18561420.17642779X-RAY DIFFRACTION98
4.4014-39.13570.1711460.17232816X-RAY DIFFRACTION95

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