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- PDB-1oga: A structural basis for immunodominant human T-cell receptor recog... -

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Basic information

Entry
Database: PDB / ID: 1oga
TitleA structural basis for immunodominant human T-cell receptor recognition.
Components
  • (T-CELL RECEPTOR ...) x 2
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • GILGFVFTL
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
KeywordsIMMUNE SYSTEM/RECEPTOR / IMMUNE SYSTEM-RECEPTOR-COMPLEX / TCR / MHC / IMMUNODOMINANCE / FLU / COMPLEX / TRANSMEMBRANE / GLYCOPROTEIN / POLYMORPHISM / T-CELL / RECEPTOR / IMMUNE SYSTEM-RECEPTOR complex
Function / homology
Function and homology information


: / : / alpha-beta T cell receptor complex / retina homeostasis / regulation of membrane depolarization / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation ...: / : / alpha-beta T cell receptor complex / retina homeostasis / regulation of membrane depolarization / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Beta-2-Microglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant / T cell receptor beta constant 1 / Beta-2-microglobulin / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsStewart-Jones, G.B.E. / McMichael, A.J. / Bell, J.I. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Nat.Immunol. / Year: 2003
Title: A Structural Basis for Immunodominant Human T Cell Receptor Recognition
Authors: Stewart-Jones, G.B.E. / Mcmichael, A.J. / Bell, J.I. / Stuart, D.I. / Jones, E.Y.
History
DepositionApr 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: GILGFVFTL
D: T-CELL RECEPTOR ALPHA CHAIN V REGION
E: T-CELL RECEPTOR BETA CHAIN C REGION


Theoretical massNumber of molelcules
Total (without water)96,9565
Polymers96,9565
Non-polymers00
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.019, 108.838, 77.741
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / MHC / A-2 ALPHA CHAIN PRECURSOR


Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR ALPHA-1, -2, -3, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin / HDCMA22P / B2M


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: BETA-2-MICROGLOBULIN, RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01884, UniProt: P61769*PLUS

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T-CELL RECEPTOR ... , 2 types, 2 molecules DE

#4: Protein T-CELL RECEPTOR ALPHA CHAIN V REGION


Mass: 23599.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CONTAINS ALSO C (CONSTANT) REGION / Source: (gene. exp.) HOMO SAPIENS (human)
Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01848*PLUS
#5: Protein T-CELL RECEPTOR BETA CHAIN C REGION / TRBC1


Mass: 28559.518 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: REFOLDED FROM INCLUSION BODIES. REFOLDED FROM INCLUSION BODIES
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BLR / References: UniProt: P01850

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Protein/peptide / Non-polymers , 2 types, 569 molecules C

#3: Protein/peptide GILGFVFTL


Mass: 966.174 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: REFOLDED FROM INCLUSION BODIES. PEPTIDE CHAIN C.REFOLDED FROM INCLUSION BODIES
Source: (synth.) HOMO SAPIENS (human)
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 41.5 %
Crystal growpH: 6.5 / Details: 14% PEG8000, 50MM MES PH 6.5
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
214 %PEG80001drop
350 mMMES1droppH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 200813 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 17.4 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.5
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Num. measured all: 3465000 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSF

1qsf


Resolution: 1.4→29.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 199296.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT WEIGHTING, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.231 9329 5 %RANDOM
Rwork0.218 ---
obs0.218 187755 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2662 Å2 / ksol: 0.371397 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.78 Å20 Å2-1.19 Å2
2--2.54 Å20 Å2
3---2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 0 568 7192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.152.5
LS refinement shellResolution: 1.4→1.45 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.371 783 5 %
Rwork0.365 14792 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 30 Å / Num. reflection obs: 178426 / Rfactor Rfree: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.369 / Rfactor Rwork: 0.364 / Num. reflection Rwork: 9329

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