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- PDB-6c61: MHC-independent T-cell receptor B12A -

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Basic information

Entry
Database: PDB / ID: 6c61
TitleMHC-independent T-cell receptor B12A
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 / Resolution: 2.43 Å
AuthorsLu, J. / Sun, P.
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 17, 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell receptor alpha chain
B: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)50,4122
Polymers50,4122
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-26 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.023, 43.630, 98.373
Angle α, β, γ (deg.)90.00, 125.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein T-cell receptor alpha chain


Mass: 22731.164 Da / Num. of mol.: 1
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: 27681.012 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 4000, 0.1M sodium acetate, pH4.6, and 0.2M (NH4)2SO4

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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: Jun 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→40 Å / Num. obs: 16078 / % possible obs: 95 % / Observed criterion σ(I): 2.1 / Redundancy: 6.6 % / Biso Wilson estimate: 59.44 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.6
Reflection shellResolution: 2.43→2.47 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.385 / Num. unique obs: 603 / % possible all: 74.8

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
SCALEITdata reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.43→39.72 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9017 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 941 5.87 %RANDOM
Rwork0.2025 ---
obs0.2053 16026 95 %-
Displacement parametersBiso mean: 62.31 Å2
Baniso -1Baniso -2Baniso -3
1-16.708 Å20 Å22.4423 Å2
2---14.3854 Å20 Å2
3----2.3226 Å2
Refine analyzeLuzzati coordinate error obs: 0.328 Å
Refinement stepCycle: 1 / Resolution: 2.43→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 0 48 3568
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013610HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.264910HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1220SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes105HARMONIC2
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it3610HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion23.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion470SEMIHARMONIC5
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_contact3939SEMIHARMONIC4
LS refinement shellResolution: 2.42→2.59 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3152 135 5.95 %
Rwork0.2339 2134 -
all0.2387 2269 -

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