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- PDB-6dkp: The complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, hum... -

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Basic information

Entry
Database: PDB / ID: 6dkp
TitleThe complex among DMF5(alpha-D26Y, alpha-Y50A,beta-L98W) TCR, human Class I MHC HLA-A2 and MART-1(26-35)(A27L) peptide
Components
  • Beta-2-microglobulin
  • DMF5 T-cell Receptor Alpha Chain fusion
  • DMF5 T-cell Receptor Beta Chain fusion
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM / Alpha-beta T-cell receptor / Class I MHC / HLA-A2 / Mart-1 peptide
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Regulation of MITF-M-dependent genes involved in pigmentation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / T cell receptor complex / 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 ...alpha-beta T cell receptor complex / Regulation of MITF-M-dependent genes involved in pigmentation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / T cell receptor complex / 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 / TAP binding / Generation of second messenger molecules / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / trans-Golgi network / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 type II interferon production / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / melanosome / Downstream TCR signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation
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 ...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 / : / Immunoglobulin V-Type / Beta-2-Microglobulin / 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 / Immunoglobulin subtype / Immunoglobulin / 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 variable 12-2 / T cell receptor beta variable 6-4 / 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 / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.966 Å
AuthorsHellman, L.M. / Singh, N.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Mol. Ther. / Year: 2019
Title: Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.
Authors: Hellman, L.M. / Foley, K.C. / Singh, N.K. / Alonso, J.A. / Riley, T.P. / Devlin, J.R. / Ayres, C.M. / Keller, G.L.J. / Zhang, Y. / Vander Kooi, C.W. / Nishimura, M.I. / Baker, B.M.
History
DepositionMay 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma antigen recognized by T-cells 1
D: DMF5 T-cell Receptor Alpha Chain fusion
E: DMF5 T-cell Receptor Beta Chain fusion


Theoretical massNumber of molelcules
Total (without water)94,0775
Polymers94,0775
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-55 kcal/mol
Surface area36520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.485, 49.063, 92.500
Angle α, β, γ (deg.)90.00, 94.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31985.398 Da / Num. of mol.: 1 / Fragment: residues 25-299
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: P01892, 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
#3: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / Antigen LB39-AA / Antigen SK29-AA / Protein Melan-A


Mass: 985.176 Da / Num. of mol.: 1 / Fragment: residues 26-35 / Mutation: A27L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655
#4: Protein DMF5 T-cell Receptor Alpha Chain fusion


Mass: 22094.412 Da / Num. of mol.: 1 / Mutation: D26Y, Y50A,D26Y, Y50A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-2, TRAC, TCRA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075B6T6, UniProt: P01848
#5: Protein DMF5 T-cell Receptor Beta Chain fusion


Mass: 27132.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-4, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0GXE1, UniProt: K7N5M4

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 12% Peg 3350, 250mM MgCl2, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.966→47.943 Å / Num. obs: 20514 / % possible obs: 94.03 % / Redundancy: 2.4 % / CC1/2: 0.996 / Net I/σ(I): 10.55
Reflection shellResolution: 2.966→3.072 Å / Num. unique obs: 5130 / CC1/2: 0.836

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L3E

4l3e


Resolution: 2.966→47.943 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 1033 5.11 %
Rwork0.2286 --
obs0.2315 20214 94.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.966→47.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6539 0 0 0 6539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026713
X-RAY DIFFRACTIONf_angle_d0.5249117
X-RAY DIFFRACTIONf_dihedral_angle_d9.0453980
X-RAY DIFFRACTIONf_chiral_restr0.041958
X-RAY DIFFRACTIONf_plane_restr0.0041194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9662-3.12250.42081530.37412774X-RAY DIFFRACTION97
3.1225-3.31810.40121640.33132761X-RAY DIFFRACTION96
3.3181-3.57420.32391170.27892754X-RAY DIFFRACTION95
3.5742-3.93380.33431480.24592666X-RAY DIFFRACTION93
3.9338-4.50260.26031250.21062694X-RAY DIFFRACTION91
4.5026-5.67140.24671730.19782764X-RAY DIFFRACTION96
5.6714-47.94890.2551530.19692768X-RAY DIFFRACTION91
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)
11.2817-0.0311.06431.5940.52951.84570.0580.3490.2005-0.09560.1168-0.1180.040.7736-00.5257-0.00950.05490.5029-0.07370.5848-37.636-13.2114-5.0061
20.8993-0.0634-0.39840.5020.16490.30450.22070.83730.5376-0.1762-0.1479-0.0180.1351-0.2790.00350.7060.093-0.03580.6250.09480.6641-60.0128-14.896-19.7358
30.0096-0.00740.00350.00050.02170.0217-0.1396-0.13570.4348-0.0748-0.2548-0.38250.08620.4820.00080.77390.01770.04740.8773-0.11050.68-33.0491-14.52711.1604
40.98460.1240.09010.3087-0.21430.30810.54810.75580.6038-0.1145-0.5872-0.3099-0.05860.8644-0.04570.62490.15920.00691.5168-0.18020.6157-10.5214-21.99765.1054
51.0339-0.20380.07790.2934-0.30650.49140.5211-0.1498-0.1680.0392-0.05640.26510.11280.54470.04490.62020.0245-0.12620.5059-0.15810.553-27.6147-30.552717.2061
60.2546-0.16990.18130.99040.66212.0221-0.06510.32860.6767-0.23430.56250.6083-0.40880.0521.22110.91410.00430.10490.83720.58021.0373-52.22090.9265-33.9559
70.3946-0.28120.03870.41960.21660.0639-0.26490.02150.16190.09030.1046-0.2502-0.52990.4849-0.00010.83420.088-0.03622.1136-0.14191.037811.9935-37.215925.6307
80.287-0.23070.11690.77350.020.24290.1563-0.8099-0.00350.314-0.02270.30820.15590.4900.82570.0332-0.12531.52460.02460.7998-2.9538-36.445635.2423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 180)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 99)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 10)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 110)
5X-RAY DIFFRACTION5(chain 'E' and resid 4 through 116)
6X-RAY DIFFRACTION6(chain 'A' and resid 181 through 275)
7X-RAY DIFFRACTION7(chain 'D' and resid 111 through 199)
8X-RAY DIFFRACTION8(chain 'E' and resid 117 through 245)

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