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- PDB-3qeq: The complex between TCR DMF4 and human Class I MHC HLA-A2 with th... -

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Basic information

Entry
Database: PDB / ID: 3qeq
TitleThe complex between TCR DMF4 and human Class I MHC HLA-A2 with the bound MART-1(27-35) nonameric peptide
Components
  • Beta-2-microglobulin
  • DMF4 alpha chain
  • DMF4 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 / 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 / Generation of second messenger molecules / TAP binding / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / trans-Golgi network / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 cellular senescence / peptide antigen binding / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / melanosome / Downstream TCR signaling / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / 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 / lysosomal membrane / external side of plasma membrane
Similarity search - Function
Protein melan-A / Protein melan-A / 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 ...Protein melan-A / Protein melan-A / 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 / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 20, 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 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 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: DMF4 alpha chain
E: DMF4 beta chain


Theoretical massNumber of molelcules
Total (without water)93,3465
Polymers93,3465
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-56 kcal/mol
Surface area38310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.651, 73.663, 225.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein DMF4 alpha chain


Mass: 21323.553 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 DMF4 beta chain


Mass: 27475.336 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, 104 molecules C

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


Mass: 813.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q16655*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
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: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→20 Å / Num. all: 31740 / Num. obs: 31613 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Χ2: 1.229 / Net I/σ(I): 25.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.59-2.646.10.28415360.675198.8
2.64-2.696.20.27615160.687198.6
2.69-2.746.10.23815470.712198.1
2.74-2.86.20.21115450.76199.7
2.8-2.866.30.18415530.818198.2
2.86-2.936.40.16815200.866199.7
2.93-36.30.14415800.902199.4
3-3.086.50.13515581.0591100
3.08-3.176.60.11315811.118199.7
3.17-3.276.70.10215511.2731100
3.27-3.396.80.09315791.341199.9
3.39-3.526.90.08216001.531199.9
3.52-3.687.10.07315541.6251100
3.68-3.887.10.07115821.549199.9
3.88-4.127.10.0715981.6731100
4.12-4.4370.06815801.6511100
4.43-4.876.70.06516101.6751100
4.87-5.576.80.06316351.6151100
5.57-6.966.90.05916401.3581100
6.96-206.30.04617481.177199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GJ6

2gj6


Resolution: 2.59→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.882 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.808 / SU B: 25.977 / SU ML: 0.256 / SU R Cruickshank DPI: 0.815 / SU Rfree: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.335 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1592 5 %RANDOM
Rwork0.215 ---
all0.218 31830 --
obs0.218 31550 99.12 %-
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: 51.31 Å2 / Biso mean: 57.631 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.59→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6576 0 0 103 6679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216756
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9289183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47423.884345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.963151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9211546
X-RAY DIFFRACTIONr_chiral_restr0.1180.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215287
X-RAY DIFFRACTIONr_mcbond_it0.491.54089
X-RAY DIFFRACTIONr_mcangle_it0.97926606
X-RAY DIFFRACTIONr_scbond_it1.62332667
X-RAY DIFFRACTIONr_scangle_it2.6524.52577
LS refinement shellResolution: 2.59→2.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 128 -
Rwork0.252 1986 -
all-2114 -
obs--92.31 %
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)
12.773-1.481-0.4434.7024-1.04633.1772-0.01120.3607-0.2467-0.0779-0.1870.32540.1761-0.34280.19820.0662-0.00960.06780.109-0.0780.141519.6711.22740.233
24.8743-3.449-2.77826.72196.062312.88040.19641.1322-0.542-0.6676-0.21560.26680.3287-0.57260.01930.49920.04030.03870.4978-0.08930.208332.02210.3387.197
36.92192.0283-2.385.8056-1.59696.45060.02650.18520.235-0.5028-0.0786-0.6952-0.33610.78410.0520.20960.03070.13830.2618-0.01220.224942.3816.04826.58
412.10253.5992-8.55021.3786-2.337810.44590.49682.15950.64570.03410.48150.4092-0.7286-2.5288-0.97830.25170.24570.10220.66440.16440.3626-5.46315.07758.796
510.0680.1225-0.98298.95863.32087.43660.713-0.46491.63780.3263-0.28660.2758-0.8055-0.6155-0.42640.3334-0.01970.25120.27550.03050.3999-20.51419.18289.139
65.33050.1365-3.24682.94222.39718.89490.1837-0.63210.16150.32710.0281-0.09070.16990.7927-0.21180.0973-0.03370.05540.1096-0.04090.154715.58517.66968.943
76.7972.7824-0.24483.2007-0.29352.28870.4276-0.6580.43410.3476-0.19020.0721-0.25720.2667-0.23750.304-0.1070.07360.1984-0.08090.132-4.55914.96792.654
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 DIFFRACTION4D2 - 112
6X-RAY DIFFRACTION5D113 - 195
7X-RAY DIFFRACTION6E1 - 112
8X-RAY DIFFRACTION7E113 - 243

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