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- PDB-3e2h: Structure of the m67 high-affinity mutant of the 2C TCR in comple... -

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Basic information

Entry
Database: PDB / ID: 3e2h
TitleStructure of the m67 high-affinity mutant of the 2C TCR in complex with Ld/QL9
Components
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • M67 TCR beta chain
  • QL9 PEPTIDE
  • T-cell receptor alpha chain V region PHDS58
KeywordsIMMUNE SYSTEM / TCR / MHC / cross-reactivity / high affinity / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Receptor
Function / homology
Function and homology information


oxoglutarate dehydrogenase (NAD+) activity / Lysine catabolism / olfactory bulb mitral cell layer development / Citric acid cycle (TCA cycle) / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation ...oxoglutarate dehydrogenase (NAD+) activity / Lysine catabolism / olfactory bulb mitral cell layer development / Citric acid cycle (TCA cycle) / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation / tangential migration from the subventricular zone to the olfactory bulb / cerebellar cortex development / pyramidal neuron development / thalamus development / 2-oxoglutarate metabolic process / striatum development / NADH metabolic process / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / thiamine pyrophosphate binding / negative regulation of natural killer cell mediated cytotoxicity / T cell receptor complex / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / tricarboxylic acid cycle / heat shock protein binding / T cell receptor binding / generation of precursor metabolites and energy / lumenal side of endoplasmic reticulum membrane / hippocampus development / mitochondrial membrane / glycolytic process / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / mitochondrion / extracellular space / metal ion binding / nucleus / plasma membrane
Similarity search - Function
2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate-binding fold / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-chain / T-cell receptor alpha chain V region PHDS58 / H-2 class I histocompatibility antigen, L-D alpha chain / 2-oxoglutarate dehydrogenase complex component E1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsColf, L.A. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2008
Title: Distinct CDR3 Conformations in TCRs Determine the Level of Cross-Reactivity for Diverse Antigens, but Not the Docking Orientation
Authors: Jones, L.L. / Colf, L.A. / Stone, J.D. / Garcia, K.C. / Kranz, D.M.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Derived calculations
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, L-D alpha chain
Q: QL9 PEPTIDE
B: T-cell receptor alpha chain V region PHDS58
C: M67 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)45,7274
Polymers45,7274
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-25 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.603, 112.603, 272.451
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 20541.621 Da / Num. of mol.: 1
Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, I66V, R97W, K131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01897
#2: Protein/peptide QL9 PEPTIDE


Mass: 1063.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN MOUSE / References: UniProt: Q60597*PLUS
#3: Protein T-cell receptor alpha chain V region PHDS58


Mass: 12211.760 Da / Num. of mol.: 1 / Mutation: L43P, W82R, G99L, F100E, A101R, S102P, A103Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01738
#4: Protein M67 TCR beta chain


Mass: 11910.015 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) / Strain (production host): BL21 / References: UniProt: A2NTY6*PLUS

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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: 5.45 Å3/Da / Density % sol: 77.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2M ammonium tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 10227 / % possible obs: 95.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.194 / Χ2: 1.095
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.366 / Num. unique all: 885 / Χ2: 1.016 / % possible all: 85.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OI9

2oi9


Resolution: 3.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.276 542 5 %
Rwork0.223 --
obs-10227 95.4 %
Solvent computationBsol: 18.359 Å2
Displacement parametersBiso max: 200 Å2 / Biso mean: 67.796 Å2 / Biso min: 3.32 Å2
Baniso -1Baniso -2Baniso -3
1-8.762 Å20 Å20 Å2
2--8.762 Å20 Å2
3----17.523 Å2
Refinement stepCycle: LAST / Resolution: 3.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 0 0 3227
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_deg1.245
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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