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- PDB-1ao7: COMPLEX BETWEEN HUMAN T-CELL RECEPTOR, VIRAL PEPTIDE (TAX), AND H... -

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Basic information

Entry
Database: PDB / ID: 1ao7
TitleCOMPLEX BETWEEN HUMAN T-CELL RECEPTOR, VIRAL PEPTIDE (TAX), AND HLA-A 0201
Components
  • (T CELL RECEPTOR ...) x 2
  • BETA-2 MICROGLOBULIN
  • HLA-A 0201
  • TAX PEPTIDE
KeywordsCOMPLEX (MHC/VIRAL PEPTIDE/RECEPTOR) / CLASS I MHC / T-CELL RECEPTOR / VIRAL PEPTIDE / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated activation of host NF-kappaB cascade / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / T cell receptor complex / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / regulation of mRNA stability / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / SH3 domain binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ETHYL MERCURY ION / : / T cell receptor alpha variable 12-2 / T cell receptor beta variable 6-5 / HLA class I histocompatibility antigen, A alpha chain / 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, HEAVY ATOM DERIVATIVES, ITERATIVE REAL-SPACE AVERAGING / Resolution: 2.6 Å
AuthorsGarboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C.
Citation
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.
#1: Journal: J.Immunol. / Year: 1996
Title: Assembly, Specific Binding, and Crystallization of a Human Tcr-Alphabeta with an Antigenic Tax Peptide from Human T Lymphotropic Virus Type 1 and the Class I Mhc Molecule Hla-A2
Authors: Garboczi, D.N. / Utz, U. / Ghosh, P. / Seth, A. / Kim, J. / Vantienhoven, E.A. / Biddison, W.E. / Wiley, D.C.
History
DepositionJul 21, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: 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 / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0267
Polymers94,5675
Non-polymers4592
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-42 kcal/mol
Surface area33490 Å2
MethodPISA
2
B: BETA-2 MICROGLOBULIN
hetero molecules

B: BETA-2 MICROGLOBULIN
hetero molecules

A: HLA-A 0201
C: TAX PEPTIDE
D: T CELL RECEPTOR ALPHA
E: T CELL RECEPTOR BETA

A: HLA-A 0201
C: TAX PEPTIDE
D: T CELL RECEPTOR ALPHA
E: T CELL RECEPTOR BETA


Theoretical massNumber of molelcules
Total (without water)190,05214
Polymers189,13310
Non-polymers9194
Water18010
TypeNameSymmetry operationNumber
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area15960 Å2
ΔGint-63 kcal/mol
Surface area67950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.300, 49.500, 96.000
Angle α, β, γ (deg.)90.00, 89.60, 90.00
Int Tables number5
Space group name H-MC121

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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: 11793.288 Da / Num. of mol.: 1 / Mutation: Y67C, K91C
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 [BV13S1] - D BETA 2.1 - J BETA 2.1 - / 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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Protein/peptide , 1 types, 1 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

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

#4: Protein T CELL RECEPTOR ALPHA


Mass: 22488.549 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 212
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 2.3 [AV2S1A2] - J ALPHA 24 - C ALPHA / 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: A0A075B6T6*PLUS
#5: Protein T CELL RECEPTOR BETA


Mass: 27360.379 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 246 / Mutation: C191A
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 [BV13S1] - D BETA 2.1 - J BETA 2.1 - C BETA 2
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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Non-polymers , 2 types, 39 molecules

#6: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5Hg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.9 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5
Details: CRYSTALLIZED FROM 10% PEG 8000, 100 MM MGACETATE, 50 MM NACACODYLATE, PH 6.5
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914
DetectorType: ADSC QUANTUM / Detector: CCD / Date: May 5, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.6→12 Å / Num. obs: 29279 / % possible obs: 95 % / Observed criterion σ(I): -3.5 / Redundancy: 3.1 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.246 / % possible all: 82.9
Reflection shell
*PLUS
% possible obs: 82.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
VECREFmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
VECREFphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, HEAVY ATOM DERIVATIVES, ITERATIVE REAL-SPACE AVERAGING
Starting model: PDB ENTRIES 1HHK, 1BEC CHAIN 1934.4

1hhk

1bec


Resolution: 2.6→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REFMAC ALSO USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 3006 10.3 %SHELLS
Rwork0.245 ---
obs0.245 29279 94.9 %-
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å20 Å20 Å2
2--6 Å20 Å2
3---6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 6 37 5711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.53
X-RAY DIFFRACTIONx_mcangle_it5.475
X-RAY DIFFRACTIONx_scbond_it5.974
X-RAY DIFFRACTIONx_scangle_it8.926
LS refinement shellResolution: 2.6→2.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.416 289 9.1 %
Rwork0.359 2878 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
LS refinement shell
*PLUS
Rfactor obs: 0.359

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