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- PDB-3d39: The complex between TCR A6 and human Class I MHC HLA-A2 with the ... -

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Basic information

Entry
Database: PDB / ID: 3d39
TitleThe complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5(4-fluoroPhenylalanine)) 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(4fluoro)F) peptide
KeywordsIMMUNE SYSTEM / HTLV-1 TAX peptide / 4-fluoroPhenylalanine / MHC class I / HLA-A2 / T-cell receptor A6 / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


alpha-beta T cell receptor complex / 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 / Translocation of ZAP-70 to Immunological synapse ...alpha-beta T cell receptor complex / 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 / 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 / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / 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 / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / 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 / 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 / Downstream TCR signaling / 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 / adaptive immune response / intracellular iron ion homeostasis / 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
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 / 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: 2.81 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 9, 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 1.2Aug 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 / pdbx_struct_special_symmetry / 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

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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(4fluoro)F) peptide
D: A6 TCR alpha chain
E: A6 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6239
Polymers94,2545
Non-polymers3684
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-57.9 kcal/mol
Surface area38180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.245, 48.320, 93.218
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-248-

GOL

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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) / References: UniProt: P01848*PLUS
#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(4fluoro)F) peptide


Mass: 1072.271 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, 57 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
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: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 15, 2005
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 24354 / Num. obs: 22601 / % possible obs: 92.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.85 / Num. unique all: 1658 / % possible all: 69

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Ice(GM/CA)data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSE

1qse


Resolution: 2.81→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 37.732 / SU ML: 0.348 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.444 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26898 1166 5.2 %RANDOM, 5.2% of the data set
Rwork0.20128 ---
all0.20479 24800 --
obs-22591 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.412 Å2
Baniso -1Baniso -2Baniso -3
1--5.12 Å20 Å21.71 Å2
2--6.39 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 24 53 6718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216845
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9369300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6225824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40523.879348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.929151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5351548
X-RAY DIFFRACTIONr_chiral_restr0.1140.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025365
X-RAY DIFFRACTIONr_nbd_refined0.1250.082484
X-RAY DIFFRACTIONr_nbtor_refined0.3230.54400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5349
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.0851
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.510
X-RAY DIFFRACTIONr_mcbond_it0.82624217
X-RAY DIFFRACTIONr_mcangle_it1.39736682
X-RAY DIFFRACTIONr_scbond_it0.69623019
X-RAY DIFFRACTIONr_scangle_it1.12732618
LS refinement shellResolution: 2.805→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 34 -
Rwork0.306 734 -
obs--42.86 %
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)
13.3327-1.01140.75862.6636-0.97253.47530.01510.2988-0.2219-0.0442-0.1430.05060.1266-0.10840.1279-0.31260.01430.0578-0.2964-0.0764-0.264637.5792-8.8029-4.2056
23.7711-0.6703-0.17866.54821.90215.24640.10821.1226-1.644-0.9593-0.2381-0.11631.2438-0.15780.12990.39360.05830.09620.4121-0.40250.340849.9907-24.8076-33.6078
35.20391.8305-1.58124.1854-1.75796.9108-0.0560.6072-0.0129-0.3874-0.0568-0.31840.08940.4690.1128-0.25740.11220.0413-0.1886-0.0381-0.28359.6338-9.2124-19.859
410.7108-2.3754-2.55171.03351.08552.20730.25780.5332-0.227-0.1907-0.21910.2822-0.1755-0.6027-0.0386-0.2528-0.0016-0.0394-0.1089-0.0943-0.18219.45851.47446.2898
58.60220.43162.717610.52822.505310.819-0.0862-0.01291.0881-0.0397-0.34440.5084-1.0051-0.48130.4306-0.11820.07820.11660.224-0.0004-0.008-12.996217.166925.0553
66.4204-2.4656-2.06335.43541.98124.71310.1423-0.25320.2740.21570.01550.077-0.17860.2308-0.1577-0.254-0.09650.0096-0.29450.0012-0.326526.315211.125620.2618
78.67352.46990.39873.81120.58523.50620.1011-0.46910.41440.1287-0.00210.1451-0.1727-0.4133-0.099-0.03990.05080.0903-0.162-0.0906-0.2312-0.135914.747835.9682
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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