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- PDB-4eup: The complex between TCR JKF6 and human Class I MHC HLA-A2 present... -

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Entry
Database: PDB / ID: 4eup
TitleThe complex between TCR JKF6 and human Class I MHC HLA-A2 presenting the MART-1(27-35)(A27L) peptide
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • JKF6 alpha chain
  • JKF6 beta chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM / nonapeptide / MHC Class I / cross-reactivity / melanoma / cancer
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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / 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 / 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 / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Protein melan-A / Protein melan-A / 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 / : ...Protein melan-A / Protein melan-A / 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
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: 2.88 Å
AuthorsHossain, M. / Baker, B.M.
CitationJournal: To be Published
Title: Structural description of how different MART-1 antigenic peptides influence JKF6 T cell receptor recognition
Authors: Hossain, M. / Baker, B.M.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Melanoma antigen recognized by T-cells 1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma antigen recognized by T-cells 1
G: JKF6 alpha chain
I: JKF6 alpha chain
H: JKF6 beta chain
J: JKF6 beta chain


Theoretical massNumber of molelcules
Total (without water)189,67910
Polymers189,67910
Non-polymers00
Water1,54986
1
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: Melanoma antigen recognized by T-cells 1
G: JKF6 alpha chain
H: JKF6 beta chain


Theoretical massNumber of molelcules
Total (without water)94,8395
Polymers94,8395
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Melanoma antigen recognized by T-cells 1
I: JKF6 alpha chain
J: JKF6 beta chain


Theoretical massNumber of molelcules
Total (without water)94,8395
Polymers94,8395
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.655, 53.700, 150.514
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules DAEBGIHJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / HLA-A*0201 heavy chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
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


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#4: Protein JKF6 alpha chain


Mass: 22472.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein JKF6 beta chain


Mass: 27777.205 Da / Num. of mol.: 2
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, 88 molecules FC

#3: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / Antigen LB39-AA / Antigen SK29-AA / Protein Melan-A


Mass: 856.062 Da / Num. of mol.: 2 / Fragment: UNP residues 27-35 / Mutation: A28L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris, 16% PEG10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 7, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.88→20 Å / Num. all: 40105 / Num. obs: 37988 / % possible obs: 93.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9
Reflection shellResolution: 2.88→2.96 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2028 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4EUR AND 2GTZ

4eur
PDB Unreleased entry

2gtz


Resolution: 2.88→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.871 / SU B: 45.048 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29488 2007 5 %RANDOM
Rwork0.23499 ---
obs0.23806 37988 92.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.65 Å2
Baniso -1Baniso -2Baniso -3
1-5.23 Å20 Å20.67 Å2
2---1.42 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13081 0 0 86 13167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213398
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.93518177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.10151621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03923.673667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.196152186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0641596
X-RAY DIFFRACTIONr_chiral_restr0.1020.21915
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110392
X-RAY DIFFRACTIONr_mcbond_it1.0271.58130
X-RAY DIFFRACTIONr_mcangle_it1.681213103
X-RAY DIFFRACTIONr_scbond_it1.59535268
X-RAY DIFFRACTIONr_scangle_it2.7854.55074
LS refinement shellResolution: 2.88→2.956 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 133 -
Rwork0.325 2408 -
obs-2408 81.23 %
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)
10.15240.1123-0.35250.4165-0.23030.9702-0.0222-0.0612-0.0608-0.001-0.0834-0.01810.05390.06810.10560.02020.0156-0.01520.06890.0260.074564.6583.42923.927
20.41050.0329-1.0482.4447-0.59392.8351-0.003-0.0125-0.0334-0.0807-0.11110.04910.0180.03840.11410.0153-0.0029-0.02410.0730.01070.058666.84419.69512.778
31.80021.1907-1.78241.3037-0.7242.1774-0.06880.0649-0.03460.0046-0.0320.01510.1328-0.08230.10080.33010.03790.01330.2996-0.00930.357329.815-28.40750.953
40.70890.2138-0.46061.1142-0.30480.9836-0.03680.1210.0822-0.09610.01380.05790.0696-0.13610.02290.24730.0216-0.03160.3182-0.00970.290519.802-11.87554.417
50.4115-0.2393-0.33060.7156-0.03430.55630.00620.0073-0.0819-0.0782-0.00940.04840.035-0.03350.00320.0489-0.0042-0.02930.0609-0.00560.0554-30.309-20.78245.471
60.4197-0.1503-1.06942.369-0.01662.82290.0101-0.0024-0.02910.0215-0.1315-0.0123-0.04610.01130.12140.026-0.0143-0.03390.0524-0.01440.0723-31.85-4.70956.633
72.674-0.8453-2.4431.37360.22413.0403-0.2126-0.133-0.2005-0.1201-0.0634-0.01770.32880.18720.2760.30910.00560.01490.23330.03560.30415.537-52.65618.9
80.963-0.5332-1.39731.39230.8283.12520.0294-0.15710.0753-0.0174-0.0811-0.1031-0.08530.36950.05170.2146-0.0682-0.0350.28470.06320.279515.259-35.74315.39
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 274
2X-RAY DIFFRACTION2E0 - 99
3X-RAY DIFFRACTION3G3 - 201
4X-RAY DIFFRACTION4H3 - 243
5X-RAY DIFFRACTION5A1 - 274
6X-RAY DIFFRACTION6B0 - 99
7X-RAY DIFFRACTION7I1 - 201
8X-RAY DIFFRACTION8J3 - 242

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