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- PDB-5bs0: MAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1 -

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Basic information

Entry
Database: PDB / ID: 5bs0
TitleMAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-1 alpha chain
  • Protein TRAV21,T-cell receptor alpha chain C region
  • Protein TRBV5-1,Human nkt tcr beta chain
  • Titin
KeywordsIMMUNE SYSTEM / Immuno pMHC TCR Titin
Function / homology
Function and homology information


sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / : / muscle alpha-actinin binding / cardiac myofibril assembly / protein kinase regulator activity ...sarcomerogenesis / titin-telethonin complex / structural molecule activity conferring elasticity / skeletal muscle myosin thick filament assembly / telethonin binding / detection of muscle stretch / : / muscle alpha-actinin binding / cardiac myofibril assembly / protein kinase regulator activity / cardiac muscle hypertrophy / cardiac muscle tissue morphogenesis / mitotic chromosome condensation / Striated Muscle Contraction / muscle filament sliding / M band / actinin binding / alpha-beta T cell receptor complex / cardiac muscle cell development / I band / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / structural constituent of muscle / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / sarcomere organization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / CD8 receptor binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / beta-2-microglobulin binding / endoplasmic reticulum exit site / striated muscle thin filament / Co-inhibition by PD-1 / skeletal muscle thin filament assembly / TAP binding / immune system process / detection of bacterium / 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 / striated muscle contraction / skeletal muscle contraction / cardiac muscle contraction / T cell receptor binding / muscle contraction / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / condensed nuclear chromosome / positive regulation of protein secretion / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / 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 erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / response to calcium ion / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / Z disc / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Similarity search - Function
PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / : / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) ...PPAK motif / PPAK motif / Titin, Z repeat / Titin Z / : / MyBP-C, tri-helix bundle domain / Tri-helix bundle domain / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin I-set / Immunoglobulin I-set domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Fibronectin type III domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Fibronectin type 3 domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Immunoglobulin V-Type / Fibronectin type III / Beta-2-Microglobulin / Fibronectin type III superfamily / : / 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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase domain / Immunoglobulin-like fold / Immunoglobulins / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 21 / T cell receptor beta variable 5-1 / Human nkt tcr beta chain / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Titin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsRaman, M.C.C. / Rizkallah, P.J. / Simmons, R. / Donellan, Z. / Dukes, J. / Bossi, G. / LeProvost, G. / Mahon, T. / Hickman, E. / Lomax, M. ...Raman, M.C.C. / Rizkallah, P.J. / Simmons, R. / Donellan, Z. / Dukes, J. / Bossi, G. / LeProvost, G. / Mahon, T. / Hickman, E. / Lomax, M. / Oates, J. / Hassan, N. / Vuidepot, A. / Sami, M. / Cole, D.K. / Jakobsen, B.K.
CitationJournal: Sci Rep / Year: 2016
Title: Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy.
Authors: Raman, M.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / Le Provost, G.S. / Todorov, P. / Baston, E. / Hickman, E. / Mahon, T. / Hassan, N. / Vuidepot, A. / ...Authors: Raman, M.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / Le Provost, G.S. / Todorov, P. / Baston, E. / Hickman, E. / Mahon, T. / Hassan, N. / Vuidepot, A. / Sami, M. / Cole, D.K. / Jakobsen, B.K.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-1 alpha chain
B: Beta-2-microglobulin
C: Titin
D: Protein TRAV21,T-cell receptor alpha chain C region
E: Protein TRBV5-1,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,36717
Polymers93,2185
Non-polymers1,14912
Water18010
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12910 Å2
ΔGint-204 kcal/mol
Surface area38660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.810, 47.480, 119.530
Angle α, β, γ (deg.)90.000, 109.360, 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-1 alpha chain / MHC class I antigen A*1


Mass: 31734.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P30443, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


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 Protein TRAV21,T-cell receptor alpha chain C region


Mass: 21451.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV21, TRAC, TCRA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279, UniProt: P01848
#5: Protein Protein TRBV5-1,Human nkt tcr beta chain / V_segment translation product


Mass: 27132.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV5S1A1T, TRBV5-1, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A578, UniProt: K7N5M4

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Titin / Connectin / Rhabdomyosarcoma antigen MU-RMS-40.14


Mass: 1021.078 Da / Num. of mol.: 1 / Fragment: UNP residues 24337-24345 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase

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Non-polymers , 3 types, 22 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Ammonium Chloride, 0.1M MES, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.13→81.82 Å / Num. all: 36248 / Num. obs: 36248 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.057 / Net I/σ(I): 11.3 / Num. measured all: 176762
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.13-2.193.80.86821438237480.5240.50197.7
9.53-81.823.40.02840.220916240.9940.01796.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.13 Å81.82 Å
Translation2.13 Å81.82 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→81.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2584 / WRfactor Rwork: 0.1963 / FOM work R set: 0.7991 / SU B: 22.195 / SU ML: 0.232 / SU R Cruickshank DPI: 0.4556 / SU Rfree: 0.2817 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.456 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 1807 5 %RANDOM
Rwork0.203 ---
obs0.206 34441 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.46 Å2 / Biso mean: 56.084 Å2 / Biso min: 21.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0 Å2-0.55 Å2
2---1.33 Å20 Å2
3---1.92 Å2
Refinement stepCycle: final / Resolution: 2.4→81.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6564 0 61 10 6635
Biso mean--83.11 37.87 -
Num. residues----822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196789
X-RAY DIFFRACTIONr_bond_other_d0.0010.026100
X-RAY DIFFRACTIONr_angle_refined_deg1.71.9439223
X-RAY DIFFRACTIONr_angle_other_deg0.894314043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2175817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98423.786346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.994151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1051553
X-RAY DIFFRACTIONr_chiral_restr0.1090.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021656
X-RAY DIFFRACTIONr_mcbond_it1.4352.3833283
X-RAY DIFFRACTIONr_mcbond_other1.4352.3833282
X-RAY DIFFRACTIONr_mcangle_it2.3593.5694095
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 138 -
Rwork0.291 2531 -
all-2669 -
obs--99.96 %
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)
13.47790.40880.22872.257-0.5653.0982-0.106-0.1641-0.13270.0032-0.0090.0309-0.08810.04630.11490.1447-0.02240.04970.1352-0.00880.030199.243738.3662278.1719
23.5625-0.11781.81925.88792.69955.385-0.3234-0.3520.96810.3848-0.07770.2636-0.6038-0.2490.40110.32960.07870.05010.4097-0.08130.329898.381652.8111311.457
32.45980.20620.24153.1793-1.10986.33120.0153-0.2321-0.19290.37320.0315-0.31680.12620.3255-0.04690.15790.00750.03830.2481-0.03130.1136113.539738.3765301.8588
44.11910.22942.68342.90260.52414.9410.0660.0172-0.0457-0.3162-0.01230.5324-0.0183-0.3551-0.05360.18590.00630.04010.2238-0.01220.171276.470333.6979254.7974
54.2321-2.7605-0.25767.51180.7633.4015-0.05-0.0168-0.4097-0.0818-0.060.49250.1175-0.27930.10990.6220.0144-0.17110.6752-0.03910.547566.372717.0469225.8527
60.33890.36680.44435.2681.63263.37630.07020.1521-0.0677-0.01830.0578-0.02070.2606-0.01-0.1280.15860.040.06350.1848-0.00850.068793.805218.3141254.776
74.5472-2.263.12424.9415-3.65965.1610.270.53070.2486-0.5741-0.21940.20670.37420.0538-0.05060.54150.04990.03270.422-0.03290.128282.756314.596226.3414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 210
7X-RAY DIFFRACTION6E0 - 115
8X-RAY DIFFRACTION7E116 - 246

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