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- PDB-4zdh: Crystal structure of JKA6 TCR -

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Basic information

Entry
Database: PDB / ID: 4zdh
TitleCrystal structure of JKA6 TCR
Components
  • Alpha chain of A6 T-cell receptor,T-cell receptor alpha chain C region
  • Beta chain of JKF6 T-cell receptor,Protein TRBV28
KeywordsIMMUNE SYSTEM / T-cell Receptor
Function / homology
Function and homology information


alpha-beta T cell receptor complex / 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 / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...alpha-beta T cell receptor complex / 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 / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / 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 C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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 12-2 / : / T cell receptor beta variable 28 / T cell receptor alpha chain constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.0984 Å
AuthorsSingh, N.K. / Hossain, M. / Baker, B.M.
CitationJournal: To Be Published
Title: Crystal structure of JKA6 TCR
Authors: Singh, N.K. / Hossain, M. / Baker, B.M.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha chain of A6 T-cell receptor,T-cell receptor alpha chain C region
B: Beta chain of JKF6 T-cell receptor,Protein TRBV28


Theoretical massNumber of molelcules
Total (without water)49,6582
Polymers49,6582
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-31 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.695, 60.087, 82.462
Angle α, β, γ (deg.)90.00, 91.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha chain of A6 T-cell receptor,T-cell receptor alpha chain C region


Mass: 22171.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Gene: TRAC, TCRA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01848, UniProt: A0A075B6T6*PLUS
#2: Protein Beta chain of JKF6 T-cell receptor,Protein TRBV28


Mass: 27486.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Gene: TRBV28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A087WZV8, UniProt: A0A5B6*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M LITHIUM SULFATE, 0.1 M TRIS-HCL, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2009 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.0984→19.49 Å / Num. obs: 25704 / % possible obs: 87.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.4
Reflection shellResolution: 2.0984→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 18.5 / % possible all: 84.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data scaling
Cootmodel building
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.0984→19.49 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1263 5.16 %Random Selection
Rwork0.1903 ---
obs0.1921 24455 95.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.0984→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 0 150 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073580
X-RAY DIFFRACTIONf_angle_d1.194852
X-RAY DIFFRACTIONf_dihedral_angle_d14.0061303
X-RAY DIFFRACTIONf_chiral_restr0.08521
X-RAY DIFFRACTIONf_plane_restr0.004636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0984-2.18230.3081300.23932163X-RAY DIFFRACTION81
2.1823-2.28150.291300.22482415X-RAY DIFFRACTION90
2.2815-2.40160.28391310.23282501X-RAY DIFFRACTION92
2.4016-2.55180.29291200.22532583X-RAY DIFFRACTION95
2.5518-2.74830.27771420.22852682X-RAY DIFFRACTION99
2.7483-3.0240.23491510.20172685X-RAY DIFFRACTION100
3.024-3.45940.20971460.18382691X-RAY DIFFRACTION99
3.4594-4.35050.19841430.16132716X-RAY DIFFRACTION100
4.3505-19.49240.1811700.1682756X-RAY DIFFRACTION100
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)
12.8705-2.6076-2.32845.45693.32792.3811-0.3325-0.3061-0.02370.29520.5692-0.20560.33970.2505-0.25260.34050.0128-0.06750.337-0.0590.277816.46315.09916.4704
24.5681-0.9628-1.23113.45081.09183.94430.03660.3605-0.3772-0.22780.0439-0.05270.226-0.0584-0.03630.3011-0.0157-0.02760.2638-0.03380.253415.9965-1.44965.6271
36.5879-4.7027-2.51095.56051.39362.46110.15220.26990.1668-0.3374-0.0376-0.0931-0.15590.1076-0.13230.2189-0.0532-0.03640.2791-0.02980.221720.90855.70194.1436
44.6423-2.9206-3.3653.34083.20264.3560.0180.3326-0.04720.1982-0.1050.0292-0.0388-0.25470.08970.2188-0.0312-0.07030.2663-0.01750.254111.11145.879710.1343
51.5006-0.5184-0.81742.93551.10432.2336-0.001-0.0903-0.3929-0.07390.2990.20740.1890.2963-0.30370.3253-0.0109-0.01930.2769-0.04630.490916.7849-12.83864.8682
65.3149-3.2093-3.6884.24633.79154.54870.1957-0.16290.4443-0.18970.0189-0.3292-0.33920.0235-0.22080.2212-0.009-0.0570.2748-0.00530.25986.199317.661621.6251
78.8063-1.3894-0.54026.38290.65316.60370.1478-1.042-0.59080.8676-0.46710.68450.168-0.9620.29420.368-0.08690.03680.4735-0.06410.3237-13.376414.608334.2245
83.66321.1404-2.59087.4843-4.03466.1197-0.2843-1.2746-0.89970.4519-0.2815-0.55030.3020.67840.56880.37410.08290.00610.62550.11860.47263.086411.355534.06
94.3056-0.3357-1.29753.283-0.74446.4098-0.0493-0.0369-0.03470.157-0.1948-0.31520.18270.09880.16430.1786-0.025-0.01770.132-0.02460.2352-3.48614.163824.7513
105.8562.5912-1.22419.39680.23736.5553-0.3215-2.2307-0.32061.4814-0.5777-0.36180.35380.42070.90441.0756-0.0932-0.15130.83670.03750.5184-4.563511.618942.1204
114.3298-4.2052-0.41794.08550.36632.06780.0388-2.28560.55891.05760.09160.1901-0.0568-0.1712-0.0250.5406-0.12370.05760.6951-0.06950.4818-3.945524.002738.0684
122.2316-0.5475-1.92452.42210.17595.246-0.0147-0.1168-0.06780.079-0.02350.08950.13220.31290.02230.2317-0.0208-0.02850.25030.00410.23743.4488-17.50468.7409
136.5241-4.0743-2.97184.98764.03963.3508-0.1869-0.5474-0.5890.54780.09720.45150.22580.11220.09580.4058-0.07430.04940.344-0.02710.3188-8.7887-13.925126.738
140.9335-0.4183-0.27763.8775-0.5811.6245-0.0599-0.07330.08510.2878-0.0522-0.24890.0910.01960.11170.1617-0.0048-0.03920.2169-0.01930.1546-10.63488.323424.8046
151.8-1.3423-0.07274.21220.24151.8143-0.0845-0.1301-0.3731-0.27360.07340.77840.4708-0.29580.0030.2772-0.09950.02110.3253-0.03210.3446-19.539-3.654122.3942
164.2196-2.71150.33363.3094-1.8561.8242-0.1524-0.29790.16040.31890.32240.8627-0.121-0.2249-0.17820.1773-0.05440.06090.3227-0.08540.2396-22.584610.729723.5619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 19 )
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 105 )
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 119 )
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 138 )
8X-RAY DIFFRACTION8chain 'A' and (resid 139 through 153 )
9X-RAY DIFFRACTION9chain 'A' and (resid 154 through 178 )
10X-RAY DIFFRACTION10chain 'A' and (resid 179 through 193 )
11X-RAY DIFFRACTION11chain 'A' and (resid 194 through 204 )
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 107 )
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 122 )
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 200 )
15X-RAY DIFFRACTION15chain 'B' and (resid 201 through 231 )
16X-RAY DIFFRACTION16chain 'B' and (resid 232 through 243 )

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