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- PDB-3utp: 1E6 TCR specific for HLA-A*0201-ALWGPDPAAA -

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Basic information

Entry
Database: PDB / ID: 3utp
Title1E6 TCR specific for HLA-A*0201-ALWGPDPAAA
Components
  • 1E6 TCR alpha chain
  • 1E6 TCR beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / Type I Diabetes
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.574 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Bulek, A.M.
CitationJournal: Nat.Immunol. / Year: 2012
Title: Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.
Authors: Bulek, A.M. / Cole, D.K. / Skowera, A. / Dolton, G. / Gras, S. / Madura, F. / Fuller, A. / Miles, J.J. / Gostick, E. / Price, D.A. / Drijfhout, J.W. / Knight, R.R. / Huang, G.C. / Lissin, N. ...Authors: Bulek, A.M. / Cole, D.K. / Skowera, A. / Dolton, G. / Gras, S. / Madura, F. / Fuller, A. / Miles, J.J. / Gostick, E. / Price, D.A. / Drijfhout, J.W. / Knight, R.R. / Huang, G.C. / Lissin, N. / Molloy, P.E. / Wooldridge, L. / Jakobsen, B.K. / Rossjohn, J. / Peakman, M. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionNov 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 1E6 TCR alpha chain
E: 1E6 TCR beta chain
K: 1E6 TCR alpha chain
L: 1E6 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,53716
Polymers101,2794
Non-polymers1,25812
Water1,49583
1
D: 1E6 TCR alpha chain
E: 1E6 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4219
Polymers50,6402
Non-polymers7827
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-82 kcal/mol
Surface area21710 Å2
MethodPISA
2
K: 1E6 TCR alpha chain
L: 1E6 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1167
Polymers50,6402
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-76 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.030, 43.260, 124.710
Angle α, β, γ (deg.)90.000, 101.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules DKEL

#1: Protein 1E6 TCR alpha chain


Mass: 22613.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
#2: Protein 1E6 TCR beta chain


Mass: 28026.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 20% w/v PEG3350, 0.2 M sodium iodide, 0.1 M Bis-tris propane, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2011 / Details: mirrors
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.574→30.578 Å / Num. all: 32433 / Num. obs: 32433 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rsym value: 0.082 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.574-2.643.60.7820.9851423580.78299.8
2.64-2.713.80.6021.2891123400.60299.9
2.71-2.793.80.5221.3830922130.522100
2.79-2.883.60.4061.7817522470.40699.9
2.88-2.973.80.2992.3795921060.29999.7
2.97-3.083.80.2273786520690.22799.8
3.08-3.193.70.1773.8728219600.17799.4
3.19-3.323.60.1464.7692919240.14699.5
3.32-3.473.60.116.2658218110.1199.5
3.47-3.643.70.0848657617700.08499.4
3.64-3.843.50.079.5583016590.0799.2
3.84-4.073.70.0610.2584215730.0699.5
4.07-4.353.70.05311.6569115250.05399.8
4.35-4.73.50.04912.9487513970.04999.6
4.7-5.153.60.04712.3455412670.04799.5
5.15-5.763.60.04712.8430011900.04799.6
5.76-6.653.60.04813.1373110320.04899.8
6.65-8.143.50.04214.731858980.04299.8
8.14-11.513.40.03812.524007040.03899.5
11.51-30.5783.30.03516.212813900.03594.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
GDAdata collection
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.574→30.578 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.2943 / WRfactor Rwork: 0.2304 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7782 / SU B: 29.459 / SU ML: 0.319 / SU R Cruickshank DPI: 1.2327 / SU Rfree: 0.3701 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.233 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1644 5.1 %RANDOM
Rwork0.2295 ---
obs0.2327 32414 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 169.82 Å2 / Biso mean: 57.8729 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å22.31 Å2
2--2.74 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.574→30.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7107 0 71 83 7261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227359
X-RAY DIFFRACTIONr_bond_other_d0.0010.025014
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.9549996
X-RAY DIFFRACTIONr_angle_other_deg0.607312168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0585888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.61824.222360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.171151191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.8621546
X-RAY DIFFRACTIONr_chiral_restr0.0740.21047
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021525
X-RAY DIFFRACTIONr_mcbond_it1.4681.54474
X-RAY DIFFRACTIONr_mcbond_other0.3511.51767
X-RAY DIFFRACTIONr_mcangle_it2.66727246
X-RAY DIFFRACTIONr_scbond_it4.1832885
X-RAY DIFFRACTIONr_scangle_it6.1764.52750
LS refinement shellResolution: 2.574→2.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 118 -
Rwork0.391 2212 -
all-2330 -
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)
15.5147-2.6851-0.03693.6956-3.69856.91580.03510.2794-0.079-0.4349-0.0693-0.00370.35980.01980.03420.1943-0.0290.02760.0339-0.01440.118847.7734-9.200219.6124
28.41410.8229-1.04497.6546-0.00874.4738-0.229-1.7704-0.0440.35520.219-0.3973-0.42031.04510.01010.2642-0.02940.01521.12310.02030.200270.1429-11.243945.8298
37.39111.36491.85114.08242.44510.33710.20890.19060.2754-0.0014-0.0888-0.2045-0.1124-0.2611-0.12010.2090.02840.04440.01730.02240.080864.7017-4.00315.6557
45.56220.1099-1.06286.9216-2.04794.9319-0.1043-1.4324-0.04320.23390.15540.017-0.16490.637-0.05110.03140.00510.00220.6342-0.04390.17179.9841-12.477632.1257
54.74-0.26092.76791.4970.30287.3727-0.0122-0.67120.23320.0952-0.04570.0608-0.11880.01070.05790.1811-0.02650.02280.1341-0.03630.11434.8255-5.986139.2787
67.9036-0.8128-2.37178.98160.60616.58860.38510.51430.6408-0.1753-0.32930.3901-0.3426-0.2325-0.05580.16760.0096-0.00780.13450.09720.133514.83925.781714.1538
75.5536-3.06492.27526.9546-2.07485.5254-0.0711-0.88480.53150.18520.07630.2522-0.38750.1309-0.00530.2671-0.11680.04630.2695-0.2030.225223.05116.401954.6392
85.56721.4068-0.19474.87132.56035.92430.26930.19870.55320.08970.04260.0291-0.4212-0.4474-0.3120.08730.06170.09240.06640.10690.32265.56498.858128.4452
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D2 - 111
2X-RAY DIFFRACTION2D114 - 200
3X-RAY DIFFRACTION3E1 - 117
4X-RAY DIFFRACTION4E121 - 246
5X-RAY DIFFRACTION5K2 - 111
6X-RAY DIFFRACTION6K114 - 202
7X-RAY DIFFRACTION7L1 - 117
8X-RAY DIFFRACTION8L121 - 246

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