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- PDB-1bd2: COMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND... -

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Basic information

Entry
Database: PDB / ID: 1bd2
TitleCOMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND MHC CLASS I MOLECULE HLA-A 0201
Components
  • (T CELL RECEPTOR ...) x 2
  • BETA-2 MICROGLOBULIN
  • HLA-A 0201
  • TAX PEPTIDE
KeywordsCOMPLEX (MHC/VIRAL PEPTIDE/RECEPTOR) / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) complex
Function / homology
Function and homology information


MHC protein binding / symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated activation of host NF-kappaB cascade / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation ...MHC protein binding / symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated activation of host NF-kappaB cascade / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / T cell receptor complex / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / regulation of mRNA stability / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / SH3 domain binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / cellular response to lipopolysaccharide / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / cell surface receptor signaling pathway
Similarity search - Function
HTLV Tax / HTLV Tax / : / : / 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 ...HTLV Tax / HTLV Tax / : / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / 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/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 beta variable 6-5 / HLA class I histocompatibility antigen, A alpha chain / T cell receptor alpha variable 29/delta variable 5 / HLA class I histocompatibility antigen, A alpha chain / Protein Tax-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human T-lymphotropic virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDing, Y.-H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Biddison, W.E. / Wiley, D.C.
Citation
Journal: Immunity / Year: 1998
Title: Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids.
Authors: Ding, Y.H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Biddison, W.E. / Wiley, D.C.
#1: Journal: Nature / Year: 1996
Title: Structure of the Complex between Human T-Cell Receptor, Viral Peptide and Hla-A2
Authors: Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C.
History
DepositionMay 12, 1998Processing site: BNL
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 1.5May 25, 2016Group: Structure summary
Revision 1.6Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-A 0201
B: BETA-2 MICROGLOBULIN
C: TAX PEPTIDE
D: T CELL RECEPTOR ALPHA
E: T CELL RECEPTOR BETA


Theoretical massNumber of molelcules
Total (without water)94,8605
Polymers94,8605
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-57 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.800, 73.300, 217.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA-A 0201 / HLA A2 HEAVY CHAIN


Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA 2, ALPHA 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: PLASMA MEMBRANE / Gene: HLA-A 0201 / Organ: PLASMA / Plasmid: PHN1
Cellular location (production host): REFOLDED FROM INCLUSION BODIES
Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein BETA-2 MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: EXTRACELLULAR / Gene: V BETA 12.3 J BETA 2.7 (BV13S1) / Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli
Cellular location (production host): REFOLDED FROM INCLUSION BODIES
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61769

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

#4: Protein T CELL RECEPTOR ALPHA


Mass: 22730.295 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cell line: BL21 / Cellular location: PLASMA MEMBRANE / Gene: V ALPHA 17.2, J ALPHA 54 (ADV21S1A1N2) / Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli
Cellular location (production host): REFOLDED FROM INCLUSION BODIES
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 338766, UniProt: P04437*PLUS
#5: Protein T CELL RECEPTOR BETA


Mass: 27326.229 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-LYMPHOCYTE / Cell line: BL21 / Cellular location: PLASMA MEMBRANE / Gene: V BETA 12.3, J BETA 2.7 (BV13S1) / Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli
Cellular location (production host): REFOLDED FROM INCLUSION BODIES
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 3002925, UniProt: A0A0K0K1A5*PLUS

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Protein/peptide / Non-polymers , 2 types, 40 molecules C

#3: Protein/peptide TAX PEPTIDE


Mass: 1070.280 Da / Num. of mol.: 1
Fragment: RESIDUES 11 - 19 FROM TAX PROTEIN OF HUMAN T LYMPHOTROPIC VIRUS TYPE 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / References: UniProt: P14079*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 58 %
Crystal growpH: 7.1
Details: 12% PEG8000, 20MM MOPS, 100MM MAGNESIUM ACETATE,PH7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Feb 5, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 33899 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.22 / % possible all: 85.1
Reflection
*PLUS
Num. measured all: 145021
Reflection shell
*PLUS
% possible obs: 85.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HHI AND 1AO7

1hhi

1ao7


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1637 5.2 %RANDOM
Rwork0.238 ---
obs0.238 31731 90.6 %-
Displacement parametersBiso mean: 41.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6339 0 0 39 6378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.421
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.252
X-RAY DIFFRACTIONx_mcangle_it5.24
X-RAY DIFFRACTIONx_scbond_it4.922
X-RAY DIFFRACTIONx_scangle_it7.334
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.42 168 4.6 %
Rwork0.38 3450 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.427
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.421

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