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Basic information

Entry
Database: PDB / ID: 3ery
TitleDifferent thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors
Components
  • 2-oxoglutarate dehydrogenase E1 peptide
  • H-2 class I histocompatibility antigen
KeywordsIMMUNE SYSTEM / MHC / Peptide recognition
Function / homology
Function and homology information


oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / tangential migration from the subventricular zone to the olfactory bulb / Lysine catabolism / cerebellar cortex development ...oxoglutarate dehydrogenase (NAD+) activity / olfactory bulb mitral cell layer development / oxoglutarate dehydrogenase (succinyl-transferring) / succinyl-CoA metabolic process / : / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / tangential migration from the subventricular zone to the olfactory bulb / Lysine catabolism / cerebellar cortex development / pyramidal neuron development / Citric acid cycle (TCA cycle) / thalamus development / 2-oxoglutarate metabolic process / striatum development / Glyoxylate metabolism and glycine degradation / 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 / 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 / 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 / mitochondrial matrix / 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 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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 / Immunoglobulin-like fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, L-D alpha chain / 2-oxoglutarate dehydrogenase complex component E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsHuang, R.H. / Jones, L.L.
CitationJournal: Biochemistry / Year: 2008
Title: Different thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors
Authors: Jones, L.L. / Colf, L.A. / Bankovich, A.J. / Stone, J.D. / Gao, Y.G. / Chan, C.M. / Huang, R.H. / Garcia, K.C. / Kranz, D.M.
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: H-2 class I histocompatibility antigen
B: H-2 class I histocompatibility antigen
P: 2-oxoglutarate dehydrogenase E1 peptide
Q: 2-oxoglutarate dehydrogenase E1 peptide


Theoretical massNumber of molelcules
Total (without water)43,0964
Polymers43,0964
Non-polymers00
Water2,540141
1
A: H-2 class I histocompatibility antigen
P: 2-oxoglutarate dehydrogenase E1 peptide


Theoretical massNumber of molelcules
Total (without water)21,5482
Polymers21,5482
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-10 kcal/mol
Surface area9690 Å2
MethodPISA
2
B: H-2 class I histocompatibility antigen
Q: 2-oxoglutarate dehydrogenase E1 peptide


Theoretical massNumber of molelcules
Total (without water)21,5482
Polymers21,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-9 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.163, 74.323, 53.255
Angle α, β, γ (deg.)90.000, 107.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein H-2 class I histocompatibility antigen


Mass: 20484.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pLM-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01897*PLUS
#2: Protein/peptide 2-oxoglutarate dehydrogenase E1 peptide / Alpha-ketoglutarate dehydrogenase


Mass: 1063.202 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide is chemically synthesized. It is found naturally in human.
References: UniProt: Q02218
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 3.5
Details: Ammonium phosphate, pH 3.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9785 Å
DetectorDetector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 23969

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.95→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 2150
RfactorNum. reflection% reflection
Rfree0.283 1694 6.6 %
Rwork0.232 --
obs-21819 85.2 %
Solvent computationBsol: 31.61 Å2
Displacement parametersBiso max: 68.74 Å2 / Biso mean: 27.584 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.883 Å20 Å2-4.843 Å2
2--3.111 Å20 Å2
3----4.994 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 0 141 2947
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.072
X-RAY DIFFRACTIONc_mcbond_it1.6271.5
X-RAY DIFFRACTIONc_scbond_it2.2312
X-RAY DIFFRACTIONc_mcangle_it2.5662
X-RAY DIFFRACTIONc_scangle_it3.2822.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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