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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-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


: / : / : / : / : / negative regulation of receptor binding / retina homeostasis / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / positive regulation of protein binding ...: / : / : / : / : / negative regulation of receptor binding / retina homeostasis / alpha-beta T cell receptor complex / positive regulation of memory T cell activation / positive regulation of protein binding / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of membrane depolarization / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / alpha-beta T cell activation / Generation of second messenger molecules / endoplasmic reticulum exit site / TAP binding / Co-inhibition by PD-1 / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / response to bacterium / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / multicellular organismal-level iron ion homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of type II interferon production / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell differentiation in thymus / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / T cell receptor signaling pathway / negative regulation of neuron projection development / Downstream TCR signaling / late endosome membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / E3 ubiquitin ligases ubiquitinate target proteins / protein refolding / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / defense response to Gram-negative bacterium / protein homotetramerization / adaptive 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

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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 / 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


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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 (eV)
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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