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- PDB-6cph: Crystal structure of the F24 TCR -

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Basic information

Entry
Database: PDB / ID: 6cph
TitleCrystal structure of the F24 TCR
Components
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / TCR / IMMUNE RECEPTOR
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell receptor complex / alpha-beta T cell activation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / peptide antigen binding / T cell receptor signaling pathway ...alpha-beta T cell receptor complex / T cell receptor complex / alpha-beta T cell activation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / peptide antigen binding / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
ACETATE ION / T cell receptor alpha variable 24 / T cell receptor beta constant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFarenc, C. / Gras, S. / Rossjohn, J.
CitationJournal: Sci Immunol / Year: 2018
Title: CD4+T cell-mediated HLA class II cross-restriction in HIV controllers.
Authors: Galperin, M. / Farenc, C. / Mukhopadhyay, M. / Jayasinghe, D. / Decroos, A. / Benati, D. / Tan, L.L. / Ciacchi, L. / Reid, H.H. / Rossjohn, J. / Chakrabarti, L.A. / Gras, S.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
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

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Assembly

Deposited unit
D: TCR alpha chain
E: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1966
Polymers50,8862
Non-polymers3104
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-61 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.124, 74.124, 193.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TCR alpha chain


Mass: 22801.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J272*PLUS
#2: Protein TCR beta chain


Mass: 28084.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris pH:8, isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→48.62 Å / Num. obs: 60317 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 21.46 Å2 / Rpim(I) all: 0.063 / Net I/σ(I): 6.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 12.9 % / Num. unique obs: 8646 / Rpim(I) all: 0.295 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KGC

1kgc


Resolution: 1.7→17.14 Å / Cor.coef. Fo:Fc: 0.9368 / Cor.coef. Fo:Fc free: 0.9205 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 2947 4.92 %RANDOM
Rwork0.2042 ---
obs0.2057 59900 99.59 %-
Displacement parametersBiso mean: 23.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.9416 Å20 Å20 Å2
2---0.9416 Å20 Å2
3---1.8833 Å2
Refine analyzeLuzzati coordinate error obs: 0.228 Å
Refinement stepCycle: 1 / Resolution: 1.7→17.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 18 449 4087
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013752HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.155123HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1285SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes552HARMONIC5
X-RAY DIFFRACTIONt_it3752HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion17.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion480SEMIHARMONIC5
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_contact4575SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2753 212 4.86 %
Rwork0.2365 4146 -
all0.2384 4358 -
obs--99.59 %

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