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- PDB-3qdj: The complex between TCR DMF5 and human Class I MHC HLA-A2 with th... -

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Entry
Database: PDB / ID: 3qdj
TitleThe complex between TCR DMF5 and human Class I MHC HLA-A2 with the bound MART-1(27-35) nonameric peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • DMF5 alpha chain
  • DMF5 beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • MART-1(27-35) peptide
KeywordsIMMUNE SYSTEM / MART-1 peptide / nonapeptide / MHC class I / HLA-A2 / TCR DMF5 / TCR DMF4 / cross-reactivity / cancer / melanoma
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding
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 / MHC class I-like antigen recognition-like ...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
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBorbulevych, O.Y. / Baker, B.M.
CitationJournal: J.Immunol. / Year: 2011
Title: TCRs Used in Cancer Gene Therapy Cross-React with MART-1/Melan-A Tumor Antigens via Distinct Mechanisms.
Authors: Borbulevych, O.Y. / Santhanagopolan, S.M. / Hossain, M. / Baker, B.M.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 17, 2011Group: Database references
Revision 1.3Sep 7, 2011Group: Database references
Revision 1.4Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: MART-1(27-35) peptide
D: DMF5 alpha chain
E: DMF5 beta chain


Theoretical massNumber of molelcules
Total (without water)93,4835
Polymers93,4835
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-56 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.774, 46.305, 85.859
Angle α, β, γ (deg.)90.000, 106.550, 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-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 / 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 / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein DMF5 alpha chain


Mass: 22007.227 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) / Strain (production host): BL21 / References: UniProt: P01848*PLUS
#5: Protein DMF5 beta chain


Mass: 26927.994 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) / Strain (production host): BL21

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Protein/peptide / Non-polymers , 2 types, 49 molecules C

#3: Protein/peptide MART-1(27-35) peptide


Mass: 813.982 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 24%, TRIS 0.1M, 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-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 38660 / Num. obs: 37500 / % possible obs: 97 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Χ2: 1.133 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.342.80.4115380.935181.5
2.34-2.383.20.43717130.942188.7
2.38-2.433.30.42117551.033190.7
2.43-2.483.40.39517731.088194.6
2.48-2.533.50.37718771.064197.1
2.53-2.593.60.32419081.059199.7
2.59-2.653.70.2818921.1061100
2.65-2.733.70.24419521.0721100
2.73-2.813.80.19119001.138199.9
2.81-2.93.80.16619361.0831100
2.9-33.80.12919061.0661100
3-3.123.80.10919491.211100
3.12-3.263.70.08619301.1671100
3.26-3.433.70.07419341.265199.9
3.43-3.653.70.05819241.268199.7
3.65-3.933.70.05219431.232199.4
3.93-4.323.60.05219171.208198.5
4.32-4.933.40.05318941.296197
4.93-6.183.50.04819221.08197.4
6.18-203.30.04819371.176194.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GJ6

2gj6


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2987 / WRfactor Rwork: 0.2439 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7284 / SU B: 27.609 / SU ML: 0.291 / SU R Cruickshank DPI: 0.4884 / SU Rfree: 0.3056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 / Stereochemistry target values: Engh & Huber / Details: U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2991 1887 5 %RANDOM, 5%
Rwork0.2404 ---
all0.2435 38804 --
obs0.2435 37477 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.75 Å2 / Biso mean: 84.271 Å2 / Biso min: 2.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.94 Å20 Å21.47 Å2
2--5.29 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 0 48 6632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216777
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9329208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.785823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20523.721344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.663151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031550
X-RAY DIFFRACTIONr_chiral_restr0.110.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215307
X-RAY DIFFRACTIONr_mcbond_it0.4731.54118
X-RAY DIFFRACTIONr_mcangle_it0.87126640
X-RAY DIFFRACTIONr_scbond_it1.47332659
X-RAY DIFFRACTIONr_scangle_it2.3554.52566
LS refinement shellResolution: 2.3→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 110 -
Rwork0.338 2086 -
all-2196 -
obs--79.51 %
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)
12.0194-0.42310.41721.22140.75423.7430.07960.2049-0.0973-0.02950.0619-0.0366-0.17190.348-0.14150.0934-0.03080.03090.1134-0.10690.121651.8256.82676.554
24.0238-1.42360.76876.8943-2.90213.42240.152-0.02960.9322-0.16040.25510.5376-0.3819-0.328-0.4070.3281-0.07310.13050.163-0.02170.39636.24421.14147.73
33.83020.88791.85572.05311.63837.6340.08520.1285-0.1263-0.07980.2080.1381-0.0277-0.1867-0.29330.0841-0.02430.05230.04810.01810.092129.4074.58261.655
45.67610.29661.37072.181-0.43213.35510.17210.4352-0.20930.0753-0.0847-0.33990.06620.7413-0.08750.1291-0.04530.03860.4724-0.17260.199780.038-0.82787.779
54.1901-0.44180.1344.4904-1.74764.31310.1594-0.1315-0.8307-0.5164-0.2431-0.73660.67640.84630.08370.52140.0506-0.0481.1586-0.16420.927100.885-17.741107.536
63.4971-1.48341.56156.5414-1.92213.64610.1147-0.4342-0.80890.51610.25660.17220.1824-0.0713-0.37140.1303-0.0731-0.00260.3173-0.10420.361662.017-10.91797.99
75.44582.13830.90743.5399-0.16282.9437-0.0656-0.1974-0.2570.04440.2135-0.1110.17790.0611-0.14780.42380.0527-0.10950.7135-0.12590.635186.173-17.313116.13
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 182
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A183 - 275
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 199
7X-RAY DIFFRACTION6E4 - 115
8X-RAY DIFFRACTION7E116 - 245

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