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- PDB-3skn: Crystal structure of the RL42 TCR unliganded -

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Basic information

Entry
Database: PDB / ID: 3skn
TitleCrystal structure of the RL42 TCR unliganded
Components
  • RL42 T cell receptor, alpha chain
  • RL42 T cell receptor, beta chain
KeywordsIMMUNE SYSTEM / T cell receptor
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 / Co-inhibition by PD-1 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway ...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 / Co-inhibition by PD-1 / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsGras, S. / Wilmann, P.G. / Zhenjun, C. / Hanim, H. / Yu Chih, L. / Kjer-Nielsen, L. / Purcell, A.W. / Burrows, S.R. / Mccluskey, J. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2012
Title: A structural basis for varied alpha-beta TCR usage against an immunodominant EBV antigen restricted to a HLA-B8 molecule.
Authors: Gras, S. / Wilmann, P.G. / Chen, Z. / Halim, H. / Liu, Y.C. / Kjer-Nielsen, L. / Purcell, A.W. / Burrows, S.R. / McCluskey, J. / Rossjohn, J.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Structure summary
Revision 1.2Sep 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RL42 T cell receptor, alpha chain
B: RL42 T cell receptor, beta chain
C: RL42 T cell receptor, alpha chain
D: RL42 T cell receptor, beta chain
E: RL42 T cell receptor, alpha chain
F: RL42 T cell receptor, beta chain
G: RL42 T cell receptor, alpha chain
H: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)200,5958
Polymers200,5958
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RL42 T cell receptor, alpha chain
D: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)50,1492
Polymers50,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-25 kcal/mol
Surface area20400 Å2
MethodPISA
3
E: RL42 T cell receptor, alpha chain
F: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)50,1492
Polymers50,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-27 kcal/mol
Surface area20430 Å2
MethodPISA
4
G: RL42 T cell receptor, alpha chain
H: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)50,1492
Polymers50,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-24 kcal/mol
Surface area20510 Å2
MethodPISA
5
A: RL42 T cell receptor, alpha chain
B: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)50,1492
Polymers50,1492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-26 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.970, 77.810, 99.640
Angle α, β, γ (deg.)69.350, 72.200, 83.330
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

#1: Protein
RL42 T cell receptor, alpha chain


Mass: 22686.078 Da / Num. of mol.: 4
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
RL42 T cell receptor, beta chain


Mass: 27462.727 Da / Num. of mol.: 4
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)
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M magnesium formate, 13% PEG 3350, pH 8, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 43561 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.699 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.9-30.5772.41167094233197.2
3-3.10.4173.27145453676197.9
3.1-3.20.2964.54126323196197.7
3.2-3.30.2285.85113042863197.6
3.3-3.40.1827.23100682553197.4
3.4-3.50.1528.4987062210198
3.5-40.11511.21319198171197.6
4-4.50.06617.24194354958197.9
4.5-50.05420.65123543182197.8
5-60.05819.61140453594198
6-100.05222.01149193863198
10-1000.04130.7439951062196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kgc

1kgc


Resolution: 2.9→45.492 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7477 / SU ML: 0.48 / σ(F): 0.02 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 2011 5.04 %
Rwork0.194 --
obs0.1989 39927 89.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.596 Å2 / ksol: 0.281 e/Å3
Displacement parametersBiso max: 261.02 Å2 / Biso mean: 61.2564 Å2 / Biso min: 3.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.482 Å2-5.5733 Å2-5.6787 Å2
2--2.5874 Å23.0767 Å2
3----5.0694 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13796 0 0 0 13796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514180
X-RAY DIFFRACTIONf_angle_d0.91819231
X-RAY DIFFRACTIONf_chiral_restr0.062055
X-RAY DIFFRACTIONf_plane_restr0.0042545
X-RAY DIFFRACTIONf_dihedral_angle_d15.7755157
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-3.00370.44391850.31923144332974
3.0037-3.12390.3961730.28723344351779
3.1239-3.26610.38261670.27283641380886
3.2661-3.43820.3811900.23413820401091
3.4382-3.65350.29212270.20293813404090
3.6535-3.93550.30592170.20213892410992
3.9355-4.33120.28892130.16833988420195
4.3312-4.95730.23422020.14364082428497
4.9573-6.24310.24532070.15454088429597
6.2431-45.49760.21112300.14684104433498
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)
10.30130.0864-0.1880.0253-0.09320.7712-0.01350.0893-0.1417-0.0025-0.01020.02090.0881-0.03330.2390.05030.02490.04940.2308-0.05030.1342-7.842749.9426-3.9821
20.86070.5257-0.17970.47780.19340.9623-0.1709-0.0547-0.1699-0.1478-0.15230.04120.03410.0147-0.00710.14380.11620.16050.23450.01880.307720.986834.12894.1674
30.6877-0.04870.2040.4626-0.4691.83260.02390.1863-0.0761-0.20190.3370.14720.4415-0.47480.27640.1415-0.1488-0.07060.24890.09670.1607-19.671929.84561.3305
40.55120.377-0.19781.1634-1.04051.3353-0.0936-0.1849-0.0071-0.1995-0.4107-0.30560.09260.408-0.19960.05410.10160.02750.1440.02310.22998.716724.68912.1024
50.57810.1862-0.08660.2847-0.34720.5785-0.14690.25970.0622-0.11530.0257-0.06740.0215-0.0950.01350.1243-0.0732-0.0217-0.0811-0.1279-0.04246.99862.9873-15.6575
60.35850.09850.12130.5118-0.09520.8552-0.233-0.0416-0.2385-0.4026-0.0835-0.44980.0279-0.1473-0.04710.3724-0.07570.34260.3443-0.02370.29253.817248.5046-36.8493
71.22540.1879-0.2331.0275-0.13591.42020.06760.03810.16990.2936-0.2457-0.1096-0.18230.4423-0.00090.1432-0.00890.01340.14230.12520.309326.665177.1007-20.3241
81.44781.0371-0.24570.8146-0.06031.0893-0.41550.2942-0.0751-0.49090.1944-0.1850.2039-0.0785-0.01410.1741-0.05590.03670.16180.03850.110711.004963.6053-43.0573
90.65560.50480.34040.79970.12660.33850.0694-0.116-0.09420.26770.1096-0.13440.05870.04070.09780.08050.04890.0559-0.0761-0.1272-0.0612-0.404463.786424.7261
100.62920.37960.24290.52790.30150.32460.3418-0.19470.00590.6362-0.1238-0.02770.5492-0.29560.02970.7731-0.31740.06220.7067-0.10120.0482-4.061159.208657.404
110.4212-0.26290.13430.5191-0.06710.1421-0.1868-0.20580.09520.14530.15290.02290.0137-0.0334-0.00470.12840.09650.07070.1462-0.10510.30949.497185.428629.064
120.95350.9022-0.1331.5913-0.02920.75570.4482-0.3310.00990.8402-0.3002-0.37660.3669-0.142-0.00970.478-0.094-0.13010.1878-0.06820.07668.240171.271256.3334
130.560.13040.20210.8116-0.40410.3874-0.04720.0407-0.0267-0.01550.0823-0.0738-0.0443-0.09120.00950.16560.0017-0.13180.04890.03740.1411-18.123751.218425.068
140.27110.0763-0.16810.5293-0.39110.41460.0776-0.07810.3333-0.02060.03050.04060.12560.38810.00020.17650.1357-0.01920.2552-0.00010.3395-29.488474.056216.2799
151.1821-0.5715-0.01231.1072-0.53841.2940.0494-0.1046-0.11780.0172-0.04860.0140.1708-0.4186-0.00740.2748-0.10170.0090.1559-0.01960.0263-36.627238.749133.9487
161.05191.1809-0.5171.3631-0.46520.5403-0.21240.12440.5454-0.24840.16660.58280.02660.0840.00530.19250.0395-0.16880.21330.09260.1373-43.246862.051915.31
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:108)A2 - 108
2X-RAY DIFFRACTION2(chain A and resid 109:198)A109 - 198
3X-RAY DIFFRACTION3(chain B and resid 2:114)B2 - 114
4X-RAY DIFFRACTION4(chain B and resid 115:242)B115 - 242
5X-RAY DIFFRACTION5(chain C and resid 2:135)C2 - 135
6X-RAY DIFFRACTION6(chain C and resid 136:198)C136 - 198
7X-RAY DIFFRACTION7(chain D and resid 2:117)D2 - 117
8X-RAY DIFFRACTION8(chain D and resid 118:242)D118 - 242
9X-RAY DIFFRACTION9(chain E and resid 2:112)E2 - 112
10X-RAY DIFFRACTION10(chain E and resid 113:198)E113 - 198
11X-RAY DIFFRACTION11(chain F and resid 2:111)F2 - 111
12X-RAY DIFFRACTION12(chain F and resid 112:242)F112 - 242
13X-RAY DIFFRACTION13(chain G and resid 2:128)G2 - 128
14X-RAY DIFFRACTION14(chain G and resid 129:198)G129 - 198
15X-RAY DIFFRACTION15(chain H and resid 2:114)H2 - 114
16X-RAY DIFFRACTION16(chain H and resid 115:242)H115 - 242

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