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- PDB-4jfh: High Affinity alpha24-beta17 T Cell Receptor for A2 HLA-Melanoma ... -

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Basic information

Entry
Database: PDB / ID: 4jfh
TitleHigh Affinity alpha24-beta17 T Cell Receptor for A2 HLA-Melanoma peptide complex
Components
  • alpha24 TCR allele
  • beta17 TCR allele
KeywordsIMMUNE SYSTEM / Immunoglobulin / HLA / TCR / Melanoma / High Affinity
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: 2.4 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Madura, F. / Sewell, A.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: T-cell receptor specificity maintained by altered thermodynamics.
Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / ...Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / Jakobsen, B.K. / Sewell, A.K. / Cole, D.K.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: alpha24 TCR allele
E: beta17 TCR allele
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,25011
Polymers49,5602
Non-polymers6919
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-58 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.140, 97.140, 123.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Antibody , 2 types, 2 molecules DE

#1: Protein alpha24 TCR allele


Mass: 22168.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01848*PLUS
#2: Antibody beta17 TCR allele


Mass: 27391.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01850*PLUS

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Non-polymers , 4 types, 170 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 20% PEG 8000, 0.2 M ammonium sulphate, pH 6.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorDetector: CCD / Date: Feb 26, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.4→49.67 Å / Num. all: 26783 / Num. obs: 26783 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Net I/σ(I): 16.6
Reflection shell

Rmerge(I) obs: 0.025 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.4611.50.22208019272.542100
2.46-2.5311.40.32184119101.759100
2.53-2.611.30.42095418501.492100
2.6-2.6810.80.41952618001.295100
2.68-2.7710.80.51889217441.002100
2.77-2.8711.50.71953417040.76100
2.87-2.9811.411854716240.545100
2.98-3.111.21.31759615780.421100
3.1-3.2410.71.81639715280.315100
3.24-3.4102.61435214360.218100
3.4-3.58113.31518113840.176100
3.58-3.810.74.51396913050.136100
3.8-4.06105.71236812320.109100
4.06-4.3810.47.51211511670.082100
4.38-4.810.881158010700.074100
4.8-5.3710.67.2103559770.081100
5.37-6.2107.285988580.086100
6.2-7.5910.98.181047420.077100
7.59-10.749.88.758135920.061100
10.74-49.66998.632123550.06199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.669 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2567 / WRfactor Rwork: 0.2027 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8409 / SU B: 12.986 / SU ML: 0.156 / SU R Cruickshank DPI: 0.2888 / SU Rfree: 0.2301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1346 5 %RANDOM
Rwork0.2005 ---
obs0.2029 26749 100 %-
all-26751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 159.8 Å2 / Biso mean: 44.6317 Å2 / Biso min: 13.27 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 41 161 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223622
X-RAY DIFFRACTIONr_bond_other_d0.0010.022449
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9464922
X-RAY DIFFRACTIONr_angle_other_deg0.68335950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.955442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.6224.629175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85915562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4091519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_mcbond_it0.9561.52218
X-RAY DIFFRACTIONr_mcbond_other0.2161.5887
X-RAY DIFFRACTIONr_mcangle_it1.84923582
X-RAY DIFFRACTIONr_scbond_it2.77631404
X-RAY DIFFRACTIONr_scangle_it4.3814.51340
LS refinement shellResolution: 2.4→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 91 -
Rwork0.286 1834 -
all-1925 -
obs--100 %
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)
11.4219-1.0786-1.67425.09242.27293.82170.07220.02530.02210.2077-0.06-0.0715-0.16220.0195-0.01220.05730.0140.00470.1030.06040.03619.864457.005652.7725
29.77012.6229-2.28979.1427-0.93338.03130.13960.19450.19540.0079-0.08010.47320.2033-1.1278-0.05940.14140.0508-0.01860.40980.02930.130512.620329.262134.502
33.62560.4424-0.34615.25581.82147.32770.03830.1980.12880.032-0.2140.2731-0.2908-0.24560.17570.01390.0045-0.00250.10310.01950.0275-4.199545.562367.5915
47.7265-1.31-1.97642.02710.17162.3373-0.08930.1962-0.3073-0.0447-0.09320.40280.27-0.43970.18250.1223-0.09190.00070.1481-0.05580.09468.400323.177448.9311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 115
2X-RAY DIFFRACTION2D116 - 200
3X-RAY DIFFRACTION3E1 - 117
4X-RAY DIFFRACTION4E118 - 244

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