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- PDB-5nht: human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptid... -

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Basic information

Entry
Database: PDB / ID: 5nht
Titlehuman 199.54-16 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 / 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 / T cell receptor complex / CD8 receptor binding ...melanosome membrane / 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 / T cell receptor complex / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / Regulation of MITF-M-dependent genes involved in pigmentation / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / immune system process / detection of bacterium / T cell receptor binding / endomembrane system / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / melanosome / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses
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 ...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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
: / THIOCYANATE ION / T cell receptor alpha variable 12-2 / TRB protein / T cell receptor beta variable 19 / T-cell receptor, sp3.4 alpha chain / 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: 3.2 Å
AuthorsExertier, C. / Reiser, J.-B. / Lantez, V. / Chouquet, A. / Bonneville, M. / Saulquin, X. / Housset, D.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV3-0006 France
CitationJournal: To Be Published
Title: human 199.54-16 TCR in complex with Melan-A/MART-1 (26-35) peptide and HLA-A2
Authors: Exertier, C. / Reiser, J.-B. / Housset, D.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 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 20, 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, sp3.4 alpha chain
B: T-cell receptor beta variable 19,TRB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4409
Polymers96,2695
Non-polymers1724
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-70 kcal/mol
Surface area37630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.077, 49.284, 96.133
Angle α, β, γ (deg.)90.00, 97.61, 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 / Fragment: UNP Residues 25-300 / 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 / Fragment: UNP Residues 25-300
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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Protein/peptide , 1 types, 1 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

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

#4: Protein T-cell receptor alpha variable 12-2,T-cell receptor, sp3.4 alpha chain / T-cell receptor / sp3.4 beta chain


Mass: 23132.400 Da / Num. of mol.: 1 / Mutation: T158C,T158C
Source method: isolated from a genetically manipulated source
Details: Numbering: residue 1 match first residue of TRAV12-2 defined in IMGT. Additional sequence in C-ter (ENDGGGCK) to enhance alpha-beta chain pairing.
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV12-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: A0A075B6T6, UniProt: K7N5N2
#5: Protein T-cell receptor beta variable 19,TRB protein / V_segment translation product


Mass: 28292.430 Da / Num. of mol.: 1
Mutation: S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C,S171C
Source method: isolated from a genetically manipulated source
Details: Numbering: residue 1 match first residue of TRBV19 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

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Non-polymers , 4 types, 5 molecules

#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350 8 %, K Thiocyanate 0.1 M, Bis-Tris propane pH 6.5 0.1 M, protein concentration 3.5 mg/ml

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979742 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2015 / Details: Si with Pt coating
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979742 Å / Relative weight: 1
ReflectionResolution: 3.2→16 Å / Num. obs: 17189 / % possible obs: 98.5 % / Redundancy: 3.66 % / Biso Wilson estimate: 62.12 Å2 / CC1/2: 0.99 / Rsym value: 0.142 / Net I/σ(I): 4.79
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.26 / Num. unique obs: 1282 / CC1/2: 0.86 / Rsym value: 0.561 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSVERSION March 1, 2015data reduction
XSCALEVERSION March 1, 2015 BUILT=20150215data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA, 3QDJ

1oga

3qdj


Resolution: 3.2→16 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.826 / SU B: 35.758 / SU ML: 0.59 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29874 796 5.1 %RANDOM
Rwork0.21293 ---
obs0.21735 14934 90.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.846 Å2
Baniso -1Baniso -2Baniso -3
1--8.71 Å20 Å2-3.9 Å2
2--6.96 Å20 Å2
3---2.69 Å2
Refinement stepCycle: 1 / Resolution: 3.2→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 6 1 6613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196787
X-RAY DIFFRACTIONr_bond_other_d0.0020.025909
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9299208
X-RAY DIFFRACTIONr_angle_other_deg0.937313748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0845819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24424350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.405151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4061546
X-RAY DIFFRACTIONr_chiral_restr0.0770.2959
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_it3.3557.4453293
X-RAY DIFFRACTIONr_mcbond_other3.3557.4483293
X-RAY DIFFRACTIONr_mcangle_it5.81111.1614107
X-RAY DIFFRACTIONr_mcangle_other5.81211.1614107
X-RAY DIFFRACTIONr_scbond_it2.637.5383493
X-RAY DIFFRACTIONr_scbond_other2.6287.5353490
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.67511.2665100
X-RAY DIFFRACTIONr_long_range_B_refined8.92384.1117412
X-RAY DIFFRACTIONr_long_range_B_other8.92384.1287413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.203→3.286 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 54 -
Rwork0.277 972 -
obs--79.35 %

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