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- PDB-2gj6: The complex between TCR A6 and human Class I MHC HLA-A2 with the ... -

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Entry
Database: PDB / ID: 2gj6
TitleThe complex between TCR A6 and human Class I MHC HLA-A2 with the modified HTLV-1 TAX (Y5K-4-[3-Indolyl]-butyric acid) peptide
Components
  • (A6-Tcr) x 2
  • Beta-2-microglobulin, Contains: Beta-2-microglobulin variant pI 5.3
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Modified HTLV-1 TAX (Y5K-IBA) peptide, chain C
KeywordsIMMUNE SYSTEM / HTLV-1 TAX peptide / haptenated peptide / Lysine-4-(3-Indolyl)-butyric acid / MHC class I / HLA-A2 / T-cell receptor A6
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 / TAP binding / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / 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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response
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 ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3-INDOLEBUTYRIC ACID / : / : / 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: 2.56 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: T Cell Receptor Recognition via Cooperative Conformational Plasticity.
Authors: Gagnon, S.J. / Borbulevych, O.Y. / Davis-Harrison, R.L. / Turner, R.V. / Damirjian, M. / Wojnarowicz, A. / Biddison, W.E. / Baker, B.M.
History
DepositionMar 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The ligand 3-indolyl-butyric acid (ligand code 3IB) undergoes substitution from LYS 5 of ...HETEROGEN The ligand 3-indolyl-butyric acid (ligand code 3IB) undergoes substitution from LYS 5 of Chain C and is missing an oxygen atom.

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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, Contains: Beta-2-microglobulin variant pI 5.3
C: Modified HTLV-1 TAX (Y5K-IBA) peptide, chain C
D: A6-Tcr
E: A6-Tcr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,09924
Polymers94,2185
Non-polymers1,88119
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)223.846, 49.019, 94.170
Angle α, β, γ (deg.)90.00, 90.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 3 molecules ABE

#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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin, Contains: Beta-2-microglobulin variant 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 / References: UniProt: P61769
#5: Protein A6-Tcr


Mass: 27360.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: GenBank: 6730544, UniProt: P01850*PLUS

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Protein/peptide / Antibody , 2 types, 2 molecules CD

#3: Protein/peptide Modified HTLV-1 TAX (Y5K-IBA) peptide, chain C


Mass: 1036.286 Da / Num. of mol.: 1 / Fragment: HTLV-1 TAX peptide / Mutation: Y5K-4-[3-Indolyl]-butyric acid / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo Sapiens (Human)
#4: Antibody A6-Tcr


Mass: 22088.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: GenBank: 6730548, UniProt: P01848*PLUS

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Non-polymers , 4 types, 108 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-3IB / 3-INDOLEBUTYRIC ACID


Mass: 203.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG8000 30%, 0.1 M Sodium Cacodylate, 0.2 M Ammonium sulfate, pH 6.5, 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: 0.9829 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 20, 2005
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9829 Å / Relative weight: 1
ReflectionResolution: 2.56→20 Å / Num. all: 32172 / Num. obs: 31915 / % possible obs: 0.992 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.4
Reflection shellResolution: 2.56→2.71 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2960 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Blu-Icedata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QSE

1qse


Resolution: 2.56→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 21.628 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.797 / ESU R Free: 0.314 / 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 1QSE, 1QRN)
RfactorNum. reflection% reflectionSelection details
Rfree0.24988 1600 5 %RANDOM; 5% of the data set
Rwork0.19949 ---
obs0.20207 30313 95.68 %-
all-33354 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.495 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å2-0.58 Å2
2--3.87 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6625 0 117 89 6831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216909
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9469372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3335822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38323.862347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.674151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0611548
X-RAY DIFFRACTIONr_chiral_restr0.1210.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025360
X-RAY DIFFRACTIONr_nbd_refined0.1280.082646
X-RAY DIFFRACTIONr_nbtor_refined0.3210.54459
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.5439
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.0858
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.514
X-RAY DIFFRACTIONr_mcbond_it0.5651.54210
X-RAY DIFFRACTIONr_mcangle_it0.98526667
X-RAY DIFFRACTIONr_scbond_it1.58633095
X-RAY DIFFRACTIONr_scangle_it2.4864.52705
LS refinement shellResolution: 2.56→2.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 50 -
Rwork0.275 1082 -
obs--47.28 %
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)
13.9397-0.3705-1.45582.33930.82.680.01190.0494-0.0606-0.0305-0.1421-0.0895-0.11130.29030.1302-0.2018-0.0024-0.0493-0.25210.0866-0.188274.25138.0341-4.408
29.4816-3.66081.49349.737-1.45157.26040.37421.41311.5875-1.1056-0.55020.0083-1.49650.2940.1760.40340.05790.04230.07960.21550.173361.593522.8908-33.8631
34.8141.36861.11983.79921.93753.8209-0.08670.3555-0.0874-0.2234-0.10030.25510.0556-0.24550.187-0.15210.0619-0.0016-0.24990.0601-0.198251.88448.2329-19.6663
413.70870.00641.10712.1261-0.87874.87610.0250.0534-0.0813-0.0144-0.0187-0.3015-0.0020.8928-0.0063-0.15940.02750.03320.05290.0103-0.1017102.3558-1.81676.229
59.05210.9443-3.971216.3703-0.840211.822-0.24110.0613-1.2685-0.6991-0.3781-0.14221.00060.7710.61930.13160.0422-0.16840.81290.08680.5163124.7624-16.819325.3311
65.5998-1.48731.24316.1964-2.52217.5905-0.0128-0.1156-0.26890.051-0.0201-0.25550.19890.20780.0329-0.1593-0.05850.0144-0.12020.0077-0.184785.5734-11.36719.7639
710.70172.3170.90024.46040.77994.3899-0.1075-0.0116-0.13760.13630.2282-0.1982-0.18770.6857-0.12080.1640.0694-0.1670.29510.1040.0545112.0867-14.07436.3523
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 DIFFRACTION6EE3 - 1163 - 114
8X-RAY DIFFRACTION7EE117 - 245116 - 244

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