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- PDB-4x6b: BK6 TCR apo structure -

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Basic information

Entry
Database: PDB / ID: 4x6b
TitleBK6 TCR apo structure
Components
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / T cell receptor / CD1a / Autoimmunity / lipid antigen
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 / Resolution: 2.1 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2015
Title: alpha beta T cell antigen receptor recognition of CD1a presenting self lipid ligands.
Authors: Birkinshaw, R.W. / Pellicci, D.G. / Cheng, T.Y. / Keller, A.N. / Sandoval-Romero, M. / Gras, S. / de Jong, A. / Uldrich, A.P. / Moody, D.B. / Godfrey, D.I. / Rossjohn, J.
History
DepositionDec 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Mar 4, 2015Group: Structure summary
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Remark 0 : statistics at the very beginning when nothing is done yet

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TCR alpha
B: TCR beta
C: TCR alpha
D: TCR beta


Theoretical massNumber of molelcules
Total (without water)101,1934
Polymers101,1934
Non-polymers00
Water12,755708
1
A: TCR alpha
B: TCR beta


Theoretical massNumber of molelcules
Total (without water)50,5962
Polymers50,5962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-24 kcal/mol
Surface area20530 Å2
MethodPISA
2
C: TCR alpha
D: TCR beta


Theoretical massNumber of molelcules
Total (without water)50,5962
Polymers50,5962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-19 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.320, 78.998, 89.590
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TCR alpha


Mass: 22998.301 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) / References: UniProt: P01848*PLUS
#2: Protein TCR beta


Mass: 27597.977 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) / References: UniProt: P01850*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M bicine, 20% PEG 6000 / PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→48.9 Å / Num. obs: 58406 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.63 Å2 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PJ5

4pj5


Resolution: 2.1→48.9 Å / Cor.coef. Fo:Fc: 0.9443 / Cor.coef. Fo:Fc free: 0.9232 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 2947 5.05 %RANDOM
Rwork0.1875 ---
obs0.1897 58326 99.89 %-
Displacement parametersBiso mean: 39.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.9421 Å20 Å21.3021 Å2
2---4.2072 Å20 Å2
3---5.1493 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: 1 / Resolution: 2.1→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 0 0 708 7413
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016887HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.089382HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2243SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1005HARMONIC5
X-RAY DIFFRACTIONt_it6887HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion16.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion891SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7521SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 196 4.56 %
Rwork0.219 4100 -
all0.2213 4296 -
obs--99.89 %
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)
11.6921-0.3174-0.41941.10630.27893.7850.17590.2623-0.0297-0.1587-0.04980.0016-0.3306-0.0463-0.1261-0.0154-0.00820.0089-0.00060.0117-0.1477-18.830315.790412.5557
23.9925-0.0110.38980.787-1.43291.77410.04710.6885-0.0478-0.0693-0.10630.1291-0.06260.4510.0592-0.0569-0.19420.0510.1957-0.1471-0.290710.48429.442816.437
31.75190.41350.53352.4358-0.04587.0735-0.11890.52970.0743-0.17680.0072-0.0277-0.10280.4950.1117-0.0318-0.16880.03320.2497-0.0768-0.122613.8827.576417.2063
41.8997-0.15680.29952.8548-0.24371.58280.04350.04440.02490.0074-0.08230.0371-0.1277-0.12920.0388-0.0524-0.01340.0072-0.0613-0.0099-0.0778-24.53418.047433.052
51.8785-0.71552.29530-1.63532.0680.05780.0115-0.20790.07410.07980.04120.2247-0.0504-0.1377-0.0679-0.01970.0165-0.13890.02860.0108-6.9704-4.931737.7617
60.5611-0.32450.38491.71330.46082.2947-0.26710.37060.0271-0.49780.29830.0701-0.34630.503-0.03110.0025-0.1295-0.0156-0.00320.0046-0.07568.54739.810930.3302
73.08962.3886-0.02033.46460.0012.3166-0.0234-0.1954-0.17140.0889-0.0209-0.0555-0.1060.37350.0443-0.0802-0.0141-0.0088-0.0640.0012-0.05845.26625.620343.1162
82.35110.1619-1.23751.070.03643.44470.22330.1311-0.073-0.0163-0.040.0563-0.3256-0.32-0.1833-0.0167-0.01750.05020.052-0.0105-0.18815.8769-24.06638.9477
94.367-0.7380.95530.0003-0.12452.1476-0.09460.5341-0.2657-0.01210.1217-0.16340.28310.212-0.0271-0.02-0.0467-0.0159-0.0428-0.1066-0.130936.5868-25.614112.4847
103.70630.5459-0.55422.89370.19865.1755-0.15230.3155-0.174-0.16440.0013-0.10630.37070.22520.151-0.0217-0.034-0.02660.0063-0.067-0.070939.9233-27.049914.3004
112.0607-0.36820.24452.8909-0.7781.6334-0.08740.1737-0.16540.0579-0.00290.0548-0.0564-0.2840.0903-0.0254-0.02010.0491-0.0092-0.0253-0.10361.6833-31.046629.6015
121.40210.81942.66810.0427-0.93171.3960.04030.0568-0.09430.12280.0765-0.1250.0946-0.048-0.1168-0.0236-0.05940.0711-0.1199-0.0046-0.00721.2262-42.061234.5111
131.55230.1417-0.81271.7833-0.37292.4516-0.18790.2063-0.1871-0.14420.12350.02590.1764-0.04220.0644-0.0629-0.0512-0.0149-0.1101-0.0351-0.088534.8384-25.847826.5155
142.63931.66570.07865.438-0.34262.43350.0377-0.1156-0.45010.38390.0099-0.12140.1704-0.1454-0.04760.0105-0.0171-0.0294-0.08450.0054-0.033732.4333-29.53139.4376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|2 - 105}
2X-RAY DIFFRACTION2{A|106 - 157}
3X-RAY DIFFRACTION3{A|158 - 202}
4X-RAY DIFFRACTION4{B|3 - 109}
5X-RAY DIFFRACTION5{B|110 - 124}
6X-RAY DIFFRACTION6{B|125 - 203}
7X-RAY DIFFRACTION7{B|204 - 244}
8X-RAY DIFFRACTION8{C|2 - 105}
9X-RAY DIFFRACTION9{C|106 - 153}
10X-RAY DIFFRACTION10{C|154 - 202}
11X-RAY DIFFRACTION11{D|3 - 109}
12X-RAY DIFFRACTION12{D|110 - 124}
13X-RAY DIFFRACTION13{D|125 - 203}
14X-RAY DIFFRACTION14{D|204 - 244}

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