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- PDB-6cuh: Crystal structure of the unliganded BC8B TCR -

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Basic information

Entry
Database: PDB / ID: 6cuh
TitleCrystal structure of the unliganded BC8B TCR
Components(T-cell Receptor ...) x 2
KeywordsIMMUNE SYSTEM / T cell receptor / TCR / BC8B / CD1b / PC / phosphatidylcholine
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsShahine, A.E. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2019
Title: A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids.
Authors: Shahine, A. / Reinink, P. / Reijneveld, J.F. / Gras, S. / Holzheimer, M. / Cheng, T.Y. / Minnaard, A.J. / Altman, J.D. / Lenz, S. / Prandi, J. / Kubler-Kielb, J. / Moody, D.B. / Rossjohn, J. / Van Rhijn, I.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell Receptor alpha variable, TRAV 9-2. BC8B TCR
B: T-cell Receptor beta variable, TRBV 6-2. BC8B TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6476
Polymers50,3252
Non-polymers3224
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Copurification as a monomer of dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-30 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.616, 76.876, 119.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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T-cell Receptor ... , 2 types, 2 molecules AB

#1: Protein T-cell Receptor alpha variable, TRAV 9-2. BC8B TCR


Mass: 22726.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein T-cell Receptor beta variable, TRBV 6-2. BC8B TCR


Mass: 27598.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 189 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.27 Å3/Da / Density % sol: 45.88 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Potassium-sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95365 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2016
RadiationMonochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.01→47.29 Å / Num. obs: 31312 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.29 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.006 / Net I/σ(I): 9.1
Reflection shellResolution: 2.01→2.07 Å / Redundancy: 7 % / Num. unique obs: 2266 / CC1/2: 0.802 / Rpim(I) all: 0.0601 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QRP, 4G8F

4qrp

4g8f


Resolution: 2.01→47.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1560 4.98 %RANDOM
Rwork0.208 ---
obs0.209 31312 100 %-
Displacement parametersBiso max: 137.14 Å2 / Biso mean: 53.68 Å2 / Biso min: 27.84 Å2
Baniso -1Baniso -2Baniso -3
1--15.4668 Å20 Å20 Å2
2--5.4458 Å20 Å2
3---10.0211 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.01→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 20 185 3466
Biso mean--76.24 53.95 -
Num. residues----427
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1492SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes496HARMONIC5
X-RAY DIFFRACTIONt_it3381HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion440SEMIHARMONIC5
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_contact3772SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3381HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4608HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion2.67
LS refinement shellResolution: 2.01→2.08 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.289 145 5.09 %
Rwork0.247 2701 -
all0.249 2846 -
obs--99.79 %
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)
10.6754-0.3319-0.02711.03870.23131.12020.0009-0.01250.02440.02030.0281-0.004-0.025-0.0171-0.02890.01430.0936-0.07830.03350.0137-0.03663.52389.6137-3.5384
21.0131-0.72360.91010.0013-0.41920.6696-0.0051-0.0158-0.001-0.03770.0148-0.0224-0.0066-0.0019-0.0096-0.0578-0.03140.00840.0350.02650.028526.3656-15.1075-8.8102
30.2717-1.5241-0.01050.9007-0.63280.75560.0039-0.02340.0016-0.07370.01120.01320.0299-0.0243-0.0150.0884-0.0942-0.152-0.07030.0508-0.0398-1.10756.2735-25.9147
40.6506-0.29420.77470.1010.97611.54220.0179-0.0596-0.0666-0.1133-0.0164-0.0027-0.0382-0.0133-0.00150.0602-0.0734-0.0861-0.07710.0652-0.055516.0156-17.8136-20.9191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - 114}A2 - 114
2X-RAY DIFFRACTION2{A|115 - 189}A115 - 189
3X-RAY DIFFRACTION3{B|2 - 115}B2 - 115
4X-RAY DIFFRACTION4{B|116 - 244}B116 - 244

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