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- PDB-5brz: MAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1 -

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Basic information

Entry
Database: PDB / ID: 5brz
TitleMAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1
Components
  • Beta-2-microglobulin
  • GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR
  • 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
KeywordsIMMUNE SYSTEM / Immuno pMHC TCR MAGE
Function / homology
Function and homology information


caspase binding / alpha-beta T cell receptor complex / negative regulation of protein processing / 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 ...caspase binding / alpha-beta T cell receptor complex / negative regulation of protein processing / 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 / T cell receptor complex / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / 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 / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / immune system process / negative regulation of autophagy / 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 / response to bacterium / peptide antigen assembly with MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / 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 / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / histone deacetylase binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / ER-Phagosome pathway / T cell receptor signaling pathway / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / : / 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 / Immunoglobulin V-Type / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 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 / Melanoma-associated antigen 3 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.62 Å
AuthorsRaman, M.C.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, Z. / Dukes, J. / Bossi, G. / LeProvost, G. / Mahon, T. / Hickman, E. / LomaX, M. ...Raman, M.C.C. / Rizkallah, P.J. / Simmons, R. / Donnellan, 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 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR
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)93,91312
Polymers93,2415
Non-polymers6727
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11840 Å2
ΔGint-154 kcal/mol
Surface area38680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.590, 47.500, 119.250
Angle α, β, γ (deg.)90.000, 109.120, 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 GLU-VAL-ASP-PRO-ILE-GLY-HIS-LEU-TYR


Mass: 1043.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43357*PLUS

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Non-polymers , 2 types, 24 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 0.1M HEPES pH7, 15% PEG 8000

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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: 2.62→82.01 Å / Num. obs: 27833 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.064 / Net I/σ(I): 12.4 / Num. measured all: 99682
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
2.62-2.693.70.9151.9744720050.450.58899.7
11.72-82.013.30.0239.711133370.9990.01393

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.62 Å82.01 Å
Translation2.62 Å82.01 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASER2.5.1phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W72 and 3O4L

1w72

3o4l


Resolution: 2.62→82.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2497 / WRfactor Rwork: 0.1761 / FOM work R set: 0.7991 / SU B: 30.693 / SU ML: 0.29 / SU R Cruickshank DPI: 0.3013 / SU Rfree: 0.3592 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 1399 5 %RANDOM
Rwork0.1934 ---
obs0.1971 26433 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.93 Å2 / Biso mean: 62.589 Å2 / Biso min: 20.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-2.06 Å2
2--2.19 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.62→82.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 35 17 6618
Biso mean--91.59 41.99 -
Num. residues----822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196771
X-RAY DIFFRACTIONr_bond_other_d0.0010.026099
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9399198
X-RAY DIFFRACTIONr_angle_other_deg0.841314040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9245817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0623.757346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.193151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7911553
X-RAY DIFFRACTIONr_chiral_restr0.0930.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217759
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021658
X-RAY DIFFRACTIONr_mcbond_it1.4032.7883283
X-RAY DIFFRACTIONr_mcbond_other1.4032.7873282
X-RAY DIFFRACTIONr_mcangle_it2.3364.1764095
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 88 -
Rwork0.315 1915 -
all-2003 -
obs--99.7 %
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)
14.06020.44760.17521.7629-0.32874.0922-0.0287-0.2311-0.130.0294-0.0214-0.01170.0907-0.1950.05010.0428-0.02280.07580.0941-0.02270.1427139.575235.6415165.2618
22.35390.40831.84616.38342.89075.3505-0.3315-0.36240.77840.4505-0.150.3405-0.898-0.52860.48150.40010.12010.07820.444-0.10140.4687138.564750.1081198.4523
32.70.0125-0.28863.5744-1.81398.0576-0.0065-0.3052-0.20890.5020.027-0.32860.16880.3443-0.02040.12720.00440.01730.1729-0.04920.2335153.665435.4344189.0251
43.76410.62733.74893.26342.43927.40660.1024-0.12960.0684-0.2642-0.16810.56680.0687-0.69760.06580.1048-0.00570.06160.27640.0190.362116.813131.2537142.131
55.2202-3.2382-0.31587.87640.24964.128-0.1507-0.0756-0.28630.20910.06870.58860.1345-0.47330.0820.5412-0.0364-0.20530.7322-0.00310.5837106.184714.6519113.1312
62.05590.93751.01476.10571.70253.99770.05280.056-0.1137-0.00920.1189-0.04060.4981-0.0266-0.17170.1570.01810.08040.15310.00340.1382134.075415.9466141.7681
75.2164-2.50463.41484.3005-4.31166.42960.24810.54840.0431-0.4169-0.13660.31580.38980.1596-0.11160.47440.00860.00970.3278-0.08330.2611122.691812.0844113.4509
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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