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- PDB-6c68: MHC-independent t cell receptor A11 -

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Basic information

Entry
Database: PDB / ID: 6c68
TitleMHC-independent t cell receptor A11
Components
  • T-cell receptor alpha chain
  • T-cell receptor beta chain
KeywordsIMMUNE SYSTEM / MHC-independent t cell receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLu, J. / Van Laethem, F. / Saba, I. / Chu, J. / Bhattacharya, A. / Love, N.C. / Tikhonova, A. / Radaev, S. / Sun, X. / Ko, A. ...Lu, J. / Van Laethem, F. / Saba, I. / Chu, J. / Bhattacharya, A. / Love, N.C. / Tikhonova, A. / Radaev, S. / Sun, X. / Ko, A. / Arnon, T. / Shifrut, E. / Friedman, N. / Weng, N. / Singer, A. / Sun, P.D.
CitationJournal: J Immunol. / Year: 2020
Title: Structure of MHC-Independent TCRs and Their Recognition of Native Antigen CD155.
Authors: Lu, J. / Van Laethem, F. / Saba, I. / Chu, J. / Tikhonova, A.N. / Bhattacharya, A. / Singer, A. / Sun, P.D.
History
DepositionJan 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 chain
B: T-cell receptor beta chain
C: T-cell receptor alpha chain
D: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)100,2234
Polymers100,2234
Non-polymers00
Water2,522140
1
A: T-cell receptor alpha chain
B: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)50,1122
Polymers50,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-27 kcal/mol
Surface area20760 Å2
MethodPISA
2
C: T-cell receptor alpha chain
D: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)50,1122
Polymers50,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-26 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 102.555, 118.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein T-cell receptor alpha chain


Mass: 23063.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein T-cell receptor beta chain


Mass: 27047.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.1M Tris, pH8.5, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 32187 / % possible obs: 94.7 % / Observed criterion σ(I): 2.1 / Redundancy: 9.9 % / Biso Wilson estimate: 69.46 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 23
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 4 % / Rmerge(I) obs: 0.487 / Num. unique obs: 1262 / % possible all: 68.4

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
SCALEITdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c5Z

3c5z


Resolution: 2.59→34.02 Å / Cor.coef. Fo:Fc: 0.9237 / Cor.coef. Fo:Fc free: 0.8898 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1619 5.04 %RANDOM
Rwork0.2018 ---
obs0.2046 32121 --
Displacement parametersBiso mean: 71.58 Å2
Baniso -1Baniso -2Baniso -3
1--17.5115 Å20 Å20 Å2
2--17.8338 Å20 Å2
3----0.3223 Å2
Refine analyzeLuzzati coordinate error obs: 0.361 Å
Refinement stepCycle: 1 / Resolution: 2.59→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6993 0 0 140 7133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017183HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.299790HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2384SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes188HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1046HARMONIC5
X-RAY DIFFRACTIONt_it7183HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion22.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion933SEMIHARMONIC5
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_contact7549SEMIHARMONIC4
LS refinement shellResolution: 2.59→2.67 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.391 108 5.96 %
Rwork0.2552 1705 -
all0.2635 1813 -

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