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- PDB-2ial: Structural basis for recognition of mutant self by a tumor-specif... -

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Basic information

Entry
Database: PDB / ID: 2ial
TitleStructural basis for recognition of mutant self by a tumor-specific, MHC class II-restricted TCR
Components
  • CD4+ T cell receptor E8 alpha chain
  • CD4+ T cell receptor E8 beta chain
KeywordsIMMUNE SYSTEM / major histocompatibility complex / T cell receptor / T cell stimulation / melanoma / tumor 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: 1.92 Å
AuthorsDeng, L. / Langley, R.J. / Mariuzza, R.A.
CitationJournal: Nat.Immunol. / Year: 2007
Title: Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor
Authors: Deng, L. / Langley, R.J. / Brown, P.H. / Xu, G. / Teng, L. / Wang, Q. / Gonzales, M.I. / Callender, G.G. / Nishimura, M.I. / Topalian, S.L. / Mariuzza, R.A.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
A: CD4+ T cell receptor E8 alpha chain
B: CD4+ T cell receptor E8 beta chain
C: CD4+ T cell receptor E8 alpha chain
D: CD4+ T cell receptor E8 beta chain


Theoretical massNumber of molelcules
Total (without water)98,9764
Polymers98,9764
Non-polymers00
Water4,378243
1
A: CD4+ T cell receptor E8 alpha chain
B: CD4+ T cell receptor E8 beta chain


Theoretical massNumber of molelcules
Total (without water)49,4882
Polymers49,4882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-28 kcal/mol
Surface area20330 Å2
MethodPISA
2
C: CD4+ T cell receptor E8 alpha chain
D: CD4+ T cell receptor E8 beta chain


Theoretical massNumber of molelcules
Total (without water)49,4882
Polymers49,4882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.044, 65.663, 84.817
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsEach asymmetric unit contains two biological units.

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Components

#1: Protein CD4+ T cell receptor E8 alpha chain


Mass: 22399.682 Da / Num. of mol.: 2 / Mutation: T156C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01848
#2: Protein CD4+ T cell receptor E8 beta chain


Mass: 27088.197 Da / Num. of mol.: 2 / Mutation: S167C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01850
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG-2000 MME, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 71032 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.1
Reflection shellResolution: 1.92→1.99 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.5 / Num. unique all: 9536 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FYT

1fyt


Resolution: 1.92→44.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.901 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26453 3496 5.1 %RANDOM
Rwork0.20753 ---
obs0.21032 65728 94.09 %-
all-69224 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.079 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6862 0 0 243 7105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0227046
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.9319599
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6475863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0724.755347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.308151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8431534
X-RAY DIFFRACTIONr_chiral_restr0.1390.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.22832
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24671
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2376
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2411.54452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02527022
X-RAY DIFFRACTIONr_scbond_it2.98833011
X-RAY DIFFRACTIONr_scangle_it4.5014.52577
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.918→1.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 220 -
Rwork0.263 3545 -
obs--70.6 %

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