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- PDB-4ftv: The complex between the high affinity version of A6 TCR (A6c134) ... -

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Basic information

Entry
Database: PDB / ID: 4ftv
TitleThe complex between the high affinity version of A6 TCR (A6c134) and human Class I MHC HLA-A2 with the bound TAX nonameric peptide
Components
  • A6 alpha chain
  • A6 beta chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Protein Tax-1
KeywordsIMMUNE SYSTEM / TAX peptide / nonapeptide / MHC class I / HLA-A2 / TCR A6 / cross-reactivity / high affinity / c134
Function / homology
Function and homology information


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 ...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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / SH3 domain binding / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
HTLV Tax / HTLV Tax / 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 / : ...HTLV Tax / HTLV Tax / 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
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-cell lymphotropic virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: To be Published
Title: Structure of a high affinity TCR reveals native binding to MHC with enhanced peptide specificity
Authors: Borbulevych, O.Y. / Baker, B.M.
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Protein Tax-1
D: A6 alpha chain
E: A6 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,24915
Polymers94,3285
Non-polymers92110
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13270 Å2
ΔGint-53 kcal/mol
Surface area38480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.230, 48.954, 94.398
Angle α, β, γ (deg.)90.000, 89.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein A6 alpha chain


Mass: 22088.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#5: Protein A6 beta chain


Mass: 27436.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Protein Tax-1 / Protein X-LOR / Trans-activating transcriptional regulatory protein of HTLV-1


Mass: 1070.280 Da / Num. of mol.: 1 / Fragment: UNP residues 11-19 / Source method: obtained synthetically / Details: commercial
Source: (synth.) Human T-cell lymphotropic virus type 1 (african isolate)
References: UniProt: P0C213

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Non-polymers , 2 types, 35 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350 24%, MES 0.025M, NaCl 0.1M, pH 6.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98494 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 12, 2008
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98494 Å / Relative weight: 1
ReflectionResolution: 2.74→20 Å / Num. all: 26730 / Num. obs: 26730 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9
Reflection shellResolution: 2.74→2.9 Å / Rmerge(I) obs: 0.557 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2546 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8062 / SU B: 34.589 / SU ML: 0.315 / SU Rfree: 0.3771 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.377 / Stereochemistry target values: Engh & Huber / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 1336 5 %RANDOM
Rwork0.2157 ---
all0.218 27372 --
obs0.218 26723 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 98.64 Å2 / Biso mean: 91.077 Å2 / Biso min: 9.03 Å2
Baniso -1Baniso -2Baniso -3
1--6.63 Å20 Å23.52 Å2
2--9.63 Å20 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.74→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 60 25 6730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216891
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9389356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62723.96351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.689151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0711547
X-RAY DIFFRACTIONr_chiral_restr0.1010.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215380
X-RAY DIFFRACTIONr_mcbond_it0.3251.54145
X-RAY DIFFRACTIONr_mcangle_it0.62526700
X-RAY DIFFRACTIONr_scbond_it0.91332746
X-RAY DIFFRACTIONr_scangle_it1.5614.52654
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 71 -
Rwork0.336 1238 -
all-1309 -
obs--67.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.71280.9380.96122.39191.08463.6861-0.0264-0.4093-0.15860.0474-0.0534-0.15570.10470.34740.07980.25030.01240.01020.13920.07860.2713-37.594-8.6744.187
29.31931.4199-1.66959.4696-2.51327.1710.0423-1.7193-1.67410.9017-0.28540.1281.41080.16750.24320.9435-0.0714-0.06920.53970.31180.5609-49.985-24.16833.959
36.8358-1.794-1.57994.77032.70745.75630.0085-0.68420.00150.488-0.07980.34880.156-0.39170.07130.3654-0.04960.00860.13680.03290.2055-59.636-8.90319.781
411.93742.2857-2.34991.5085-0.87481.74580.1379-0.1717-0.05460.2226-0.2446-0.4654-0.1781.06830.10660.2672-0.0577-0.05980.88340.08260.3879-9.4531.881-6.368
55.0976-2.18622.338611.766-3.082810.0412-0.19450.04850.90490.4404-0.2308-0.1425-0.6820.4910.42520.9293-0.1280.09951.64350.00931.127912.63317.53-25.504
66.00070.7851-0.86167.2537-3.86116.47650.16740.16260.4732-0.1934-0.0476-0.0954-0.34550.1445-0.11970.3406-0.01730.030.16390.02670.2355-26.54212.198-20.568
711.6859-3.707-2.13115.37550.99095.1719-0.1379-0.20280.01820.00640.3376-0.1378-0.11620.9432-0.19980.589-0.11740.14490.65390.15390.454-0.53814.942-36.448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A183 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 116
6X-RAY DIFFRACTION5D117 - 206
7X-RAY DIFFRACTION6E3 - 116
8X-RAY DIFFRACTION7E117 - 246

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