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- PDB-3d3v: The complex between TCR A6 and human Class I MHC HLA-A2 with the ... -

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Entry
Database: PDB / ID: 3d3v
TitleThe complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5(3,4-difluoroPhenylalanine)) peptide
Components
  • A6 TCR alpha chain
  • A6 TCR beta chain
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Modified HTLV-1 TAX (Y5(3,4-difluoro)F) peptide
KeywordsIMMUNE SYSTEM / HTLV-1 TAX peptide / 3 / 4-difluoroPhenylalanine / MHC class I / HLA-A2 / T-cell receptor A6 / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Secreted / Disease mutation / Glycation / Pyrrolidone carboxylic acid
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / 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 / Translocation of ZAP-70 to Immunological synapse ...alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / 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 / 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 / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Generation of second messenger molecules / TAP binding / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / immunoglobulin complex, circulating / immunoglobulin receptor binding / 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 / DAP12 interactions / negative regulation of receptor binding / complement activation, classical pathway / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / blood microparticle / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen
Similarity search - Function
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 ...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 beta constant 1 / 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: 2.8 Å
AuthorsBorbulevych, O.Y. / Clemens, J.R. / Baker, B.M.
CitationJournal: Biochem.J. / Year: 2009
Title: Fluorine substitutions in an antigenic peptide selectively modulate T-cell receptor binding in a minimally perturbing manner.
Authors: Piepenbrink, K.H. / Borbulevych, O.Y. / Sommese, R.F. / Clemens, J. / Armstrong, K.M. / Desmond, C. / Do, P. / Baker, B.M.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: Modified HTLV-1 TAX (Y5(3,4-difluoro)F) peptide
D: A6 TCR alpha chain
E: A6 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,82511
Polymers94,2725
Non-polymers5536
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-56 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.450, 48.537, 93.794
Angle α, β, γ (deg.)90.00, 90.61, 90.00
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
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein A6 TCR 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)
#5: Protein A6 TCR beta chain


Mass: 27360.379 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) / References: UniProt: P01850*PLUS

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Modified HTLV-1 TAX (Y5(3,4-difluoro)F) peptide


Mass: 1090.261 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence from viral protein HTLV-1 TAX. The peptide is commercially available

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Non-polymers , 2 types, 33 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: TRIS 0.1 M, PEG4000 15%, MgCl2 0.2M, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 21, 2006
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.87→20 Å / Num. all: 25184 / Num. obs: 25084 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26.9
Reflection shellResolution: 2.87→2.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2399 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSE

1qse


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / SU B: 47.788 / SU ML: 0.42 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.424 / Stereochemistry target values: Engh & Huber
Details: Residue numbering for the chains D,E (A6 TCR) has been chosen to match with previously published TCR A6 structures (PDB Entries e.g. 1QSE, 1QRN)
RfactorNum. reflection% reflectionSelection details
Rfree0.27787 1277 5.1 %RANDOM, 5.1% of the data set
Rwork0.22041 ---
all0.22351 25316 --
obs-24962 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.751 Å2
Baniso -1Baniso -2Baniso -3
1--6.13 Å20 Å2-1.94 Å2
2--12.24 Å20 Å2
3----6.15 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 36 27 6705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216884
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9399351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11623.818351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.858151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5181550
X-RAY DIFFRACTIONr_chiral_restr0.1220.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025389
X-RAY DIFFRACTIONr_nbd_refined0.1290.082574
X-RAY DIFFRACTIONr_nbtor_refined0.330.54396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.5317
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.0842
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.57
X-RAY DIFFRACTIONr_mcbond_it0.96324231
X-RAY DIFFRACTIONr_mcangle_it1.59436694
X-RAY DIFFRACTIONr_scbond_it0.75523058
X-RAY DIFFRACTIONr_scangle_it1.14532657
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.517 77 -
Rwork0.36 1442 -
obs--83.23 %
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)
13.3061.2411-1.02612.771-0.70284.0635-0.1319-0.45320.33080.06510.06260.1232-0.1207-0.21140.0693-0.3090.0182-0.0384-0.426-0.0567-0.199637.6213-15.52254.1986
24.90791.02590.78597.46362.01434.6979-0.1669-1.24691.60550.8587-0.23480.0878-1.30160.03090.40160.4973-0.08790.01970.5577-0.32220.203950.34370.136433.6643
36.3257-1.70960.71643.7008-2.04657.1523-0.081-1.02310.15090.51560.0164-0.3508-0.08260.84220.0646-0.1785-0.0574-0.056-0.1622-0.0746-0.257959.7885-15.245819.7148
414.11491.89552.58381.45160.98892.580.1579-0.34410.35670.2329-0.25870.23080.197-0.92060.1009-0.2777-0.04030.1218-0.0412-0.0478-0.20149.4165-25.6006-6.2616
57.5526-1.2136-3.25669.91261.57110.922-0.2802-0.0773-1.00650.4477-0.23290.72461.4046-0.36780.5131-0.0007-0.1156-0.15680.69890.06490.3242-12.6699-41.3055-25.439
67.25352.96112.30876.30353.44167.3826-0.01690.2949-0.3601-0.0040.13910.06640.31050.4647-0.1222-0.16550.1010.006-0.44250.0422-0.215826.3058-34.8361-19.8598
79.8688-1.93351.81473.687-0.81273.7331-0.2640.067-0.1631-0.02010.23630.02690.2888-0.85470.02770.0753-0.0406-0.1370.0978-0.1465-0.18850.5017-38.8569-36.2488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1821 - 182
2X-RAY DIFFRACTION1CC1 - 91 - 9
3X-RAY DIFFRACTION2AA183 - 275183 - 275
4X-RAY DIFFRACTION3BB0 - 991 - 100
5X-RAY DIFFRACTION4DD1 - 1161 - 110
6X-RAY DIFFRACTION5DD117 - 200111 - 194
7X-RAY DIFFRACTION6EE1 - 1161 - 114
8X-RAY DIFFRACTION7EE117 - 245116 - 244

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