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

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Basic information

Entry
Database: PDB / ID: 3qdg
TitleThe complex between TCR DMF5 and human Class I MHC HLA-A2 with the bound MART-1(26-35)(A27L) peptide
Components
  • Beta-2-microglobulin
  • DMF5 alpha chain
  • DMF5 beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Mart-1 (26-35) peptide
KeywordsIMMUNE SYSTEM / Mart-1 peptide / decapeptide / MHC class I / HLA-A2 / TCR DMF5 / cross-reactivity / melanoma / cancer
Function / homology
Function and homology information


alpha-beta T cell receptor complex / 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 / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse ...alpha-beta T cell receptor complex / 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 / 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 / T cell receptor binding / 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 / 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 / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / endoplasmic reticulum membrane / Neutrophil degranulation
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 / : ...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 / Immunoglobulin-like fold / Immunoglobulins / 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 / Resolution: 2.69 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
Revision 1.5Nov 6, 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-2 alpha chain
B: Beta-2-microglobulin
C: Mart-1 (26-35) peptide
D: DMF5 alpha chain
E: DMF5 beta chain


Theoretical massNumber of molelcules
Total (without water)93,6545
Polymers93,6545
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-57 kcal/mol
Surface area37480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.361, 46.554, 86.036
Angle α, β, γ (deg.)90.000, 106.730, 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 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) / 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)

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Protein/peptide / Non-polymers , 2 types, 25 molecules C

#3: Protein/peptide Mart-1 (26-35) peptide


Mass: 985.176 Da / Num. of mol.: 1 / Mutation: A27L / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 30%, 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 / Date: Oct 15, 2009
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→20 Å / Num. all: 24430 / Num. obs: 22060 / % possible obs: 90.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.079 / Χ2: 1.313 / Net I/σ(I): 18.18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.69-2.752.70.2697511.027162.2
2.75-2.82.70.2488571.102170.7
2.8-2.852.90.2398861.081174.4
2.85-2.912.90.2349421.028178
2.91-2.973.10.22410721.068187.3
2.97-3.043.20.19210941.114191.6
3.04-3.123.30.18211361.08192.6
3.12-3.23.50.16111781.079198.7
3.2-3.293.60.13611881.099198.3
3.29-3.43.60.12411981.15198.8
3.4-3.523.60.11112321.303199.4
3.52-3.663.50.09411911.483199.2
3.66-3.833.40.0911911.632198
3.83-4.033.20.07211711.59196.6
4.03-4.2830.06311761.539194.4
4.28-4.62.80.05711011.749190.7
4.6-5.062.70.05211081.715189.9
5.06-5.772.90.05111681.692193.4
5.77-7.223.10.05112021.41197.3
7.22-202.80.04812181.216193.4

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Processing

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

2gj6


Resolution: 2.69→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.2882 / WRfactor Rwork: 0.2207 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.76 / SU B: 42.879 / SU ML: 0.374 / SU Rfree: 0.4428 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.443 / Stereochemistry target values: Engh & Huber / Details: U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 1123 5.1 %RANDOM, 5%
Rwork0.2179 ---
all0.221 24453 --
obs0.221 22059 90.21 %-
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 max: 65.14 Å2 / Biso mean: 91.254 Å2 / Biso min: 8.27 Å2
Baniso -1Baniso -2Baniso -3
1--8.01 Å20 Å23.01 Å2
2--6.78 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 2.69→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6596 0 0 24 6620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216788
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9329223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77323.739345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.392151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1681550
X-RAY DIFFRACTIONr_chiral_restr0.0950.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215315
X-RAY DIFFRACTIONr_mcbond_it0.54324122
X-RAY DIFFRACTIONr_mcangle_it0.9736648
X-RAY DIFFRACTIONr_scbond_it0.522666
X-RAY DIFFRACTIONr_scangle_it0.81132573
LS refinement shellResolution: 2.69→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 65 -
Rwork0.328 1037 -
all-1102 -
obs--62.72 %
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)
12.5933-0.82580.34481.25531.22574.77270.12060.1768-0.121-0.05330.1299-0.073-0.21350.487-0.25050.2454-0.0631-0.00120.1965-0.16530.161551.7726.95776.674
25.7731-0.62230.17796.1482-2.42142.80280.23910.22311.578-0.24430.23650.5076-0.4015-0.2138-0.47550.5351-0.08990.16610.15660.04750.569236.11921.23747.547
34.12760.49271.89372.63582.22997.59770.07960.1475-0.0809-0.16720.26240.196-0.0002-0.2269-0.3420.2779-0.06860.02050.09180.05340.101229.2424.70161.702
47.07910.49491.02182.0099-1.13723.67040.2850.6847-0.46430.1142-0.2797-0.3660.10021.0305-0.00530.2743-0.0801-0.00890.7358-0.25680.241880.018-0.85787.931
54.9866-0.7401-0.15426.6562-2.92094.3571-0.06890.2312-0.8602-0.3541-0.4961-0.73040.60610.68720.5650.58060.0474-0.04231.1737-0.11391.0004100.741-17.973107.631
63.9982-2.0462.87578.8924-2.79554.09990.2116-0.4916-0.80720.49330.32560.36090.2544-0.0239-0.53720.2873-0.0876-0.02640.4214-0.15310.424261.979-11.02998.078
76.99862.6521.27214.7286-0.61433.9909-0.2255-0.3681-0.19790.00290.2157-0.00190.09-0.09040.00980.57880.0233-0.10290.6943-0.07440.565986.039-17.604116.34
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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