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- PDB-5nqk: human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide a... -

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Basic information

Entry
Database: PDB / ID: 5nqk
Titlehuman 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM / Melan-A/MART-1 PEPTIDE / DECAPEPTIDE / MHC CLASS I / HLA-A2 / T cell receptor
Function / homology
Function and homology information


melanosome membrane / 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 / T cell receptor complex / 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 ...melanosome membrane / 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 / T cell receptor complex / 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 / Regulation of MITF-M-dependent genes involved in pigmentation / immune system process / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / TAP binding / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / 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 / T cell receptor binding / detection of bacterium / : / : / 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 / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / trans-Golgi network / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / antibacterial humoral response / Downstream TCR signaling / tertiary granule lumen / melanosome / DAP12 signaling / positive regulation of protein binding / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium
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 / Immunoglobulin V-set domain / 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 beta variable 19 / T cell receptor alpha variable 12-2 / T cell receptor alpha joining 45 / TRB protein / : / T cell receptor beta variable 19 / 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: 3.25 Å
AuthorsExertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D.
CitationJournal: To Be Published
Title: human 199.16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Authors: Exertier, C. / Reiser, J.-B. / Housset, D.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 1.2Nov 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
H: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
P: Melanoma antigen recognized by T-cells 1
A: T-cell receptor alpha variable 12-2,T-cell receptor alpha joining 45,T-cell receptor alpha chain C region
B: T-cell receptor beta variable 19,TRB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2506
Polymers96,2275
Non-polymers231
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-68 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.180, 49.720, 95.720
Angle α, β, γ (deg.)90.00, 97.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules HL

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


Mass: 31979.367 Da / Num. of mol.: 1 / Mutation: A245V
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) / Variant (production host): X90F LAQQ1 / 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 / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Variant (production host): X90F LAQQ1 / References: UniProt: P61769

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T-cell receptor ... , 2 types, 2 molecules AB

#4: Protein T-cell receptor alpha variable 12-2,T-cell receptor alpha joining 45,T-cell receptor alpha chain C region / 199.54 TCR ALPHA CHAIN (TRAJ 12-2 / TRAJ 45) / T-CELL RECEPTOR / 199.54 TCR ALPHA CHAIN (TRAJ 12-2 / TRAJ 45)


Mass: 23090.320 Da / Num. of mol.: 1 / Mutation: T158C,T158C,T158C
Source method: isolated from a genetically manipulated source
Details: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRAV 12-2 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (ENDGGGCK) TO ENHANCE ALPHA-BETA CHAIN PAIRING.
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-2, TRAJ45, TRAC / Plasmid: pJEXPRESS414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL
References: UniProt: A0A075B6T6, UniProt: A0A075B6X0, UniProt: A0A1B0GUM0, UniProt: P01848*PLUS
#5: Protein T-cell receptor beta variable 19,TRB protein / V_SEGMENT TRANSLATION PRODUCT / 199.16 TCR BETA CHAIN (TRBV 19 / TRBD2 / TRBJ 2-2 / TRBC2) / 199.16 ...V_SEGMENT TRANSLATION PRODUCT / 199.16 TCR BETA CHAIN (TRBV 19 / TRBD2 / TRBJ 2-2 / TRBC2) / 199.16 TCR BETA CHAIN (TRBV 19 / TRBD2 / TRBJ 2-2 / TRBC2)


Mass: 28292.430 Da / Num. of mol.: 1 / Mutation: S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C
Source method: isolated from a genetically manipulated source
Details: NUMBERING: RESIDUE 1 MATCH FIRST RESIDUE OF TRBV 19 DEFINED IN IMGT. ADDITIONAL SEQUENCE IN C-TER (DQDRGGGCD) TO ENHANCE ALPHA-BETA CHAIN PAIRING.
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV17S1A1T, TRBV19, TRB / Plasmid: pJEXPRESS414 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL
References: UniProt: A0A5B3, UniProt: A0A0C4ZKA8, UniProt: A0A075B6N1*PLUS

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Protein/peptide / Non-polymers , 2 types, 2 molecules P

#3: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / ANTIGEN LB39-AA / ANTIGEN SK29-AA / PROTEIN MELAN-A / MELAN-A/MART-1 (26-35) DECAPEPTIDE


Mass: 985.176 Da / Num. of mol.: 1 / Mutation: A27L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655*PLUS
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350 11%, bis-tris propane pH 6.5 0.1M, KNa tartrate 0.1M

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.25→48.53 Å / Num. obs: 16830 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rsym value: 0.173 / Net I/σ(I): 6.28
Reflection shellResolution: 3.25→3.33 Å / Redundancy: 3.43 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1236 / CC1/2: 0.523 / Rsym value: 1.611 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
XSCALEVERSION Nov 1, 2016 BUILT=20161205data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NHT

5nht


Resolution: 3.25→48.53 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / SU B: 50.604 / SU ML: 0.742 / Cross valid method: THROUGHOUT / ESU R Free: 0.759 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31617 722 5 %RANDOM
Rwork0.22357 ---
obs0.22803 13863 85.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 109.51 Å2
Baniso -1Baniso -2Baniso -3
1--8.71 Å20 Å2-5.34 Å2
2--9.62 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 3.25→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 1 0 6604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196782
X-RAY DIFFRACTIONr_bond_other_d0.0020.025903
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9299202
X-RAY DIFFRACTIONr_angle_other_deg0.926313735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8045819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35524350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.28151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4361546
X-RAY DIFFRACTIONr_chiral_restr0.0770.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217639
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021467
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.22711.1143292
X-RAY DIFFRACTIONr_mcbond_other5.22711.1163293
X-RAY DIFFRACTIONr_mcangle_it8.8316.6564107
X-RAY DIFFRACTIONr_mcangle_other8.82916.6564107
X-RAY DIFFRACTIONr_scbond_it4.29911.373490
X-RAY DIFFRACTIONr_scbond_other4.29911.3683488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.46516.9415095
X-RAY DIFFRACTIONr_long_range_B_refined12.6517326
X-RAY DIFFRACTIONr_long_range_B_other12.657327
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.248→3.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 37 -
Rwork0.483 768 -
obs--64.14 %

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