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- PDB-5men: Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with... -

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Entry
Database: PDB / ID: 5men
TitleHuman Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • ILE-LEU-ALA-LYS-PHE-LEU-HIS-TRP-LEU
  • Protein TRAV22,Human nkt tcr alpha chain
  • Protein TRBV6-5,Human nkt tcr beta chain
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase activity / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / telomerase activity / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / siRNA processing / nuclear telomere cap complex / telomere maintenance via recombination / positive regulation of vascular associated smooth muscle cell migration / telomerase holoenzyme complex / telomerase RNA binding / 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 / DNA biosynthetic process / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell receptor complex / RNA-templated transcription / CD8 receptor binding / positive regulation of stem cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class I / telomeric DNA binding / beta-2-microglobulin binding / endoplasmic reticulum exit site / 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 / mitochondrial nucleoid / negative regulation of cellular senescence / replicative senescence / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / Telomere Extension By Telomerase / immune system process / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of G1/S transition of mitotic cell cycle / response to cadmium ion / positive regulation of Wnt signaling pathway / positive regulation of protein binding / detection of bacterium / negative regulation of endothelial cell apoptotic process / telomere maintenance via telomerase / T cell receptor binding / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / 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 / positive regulation of D-glucose import across plasma membrane / Endosomal/Vacuolar pathway / mitochondrion organization / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / 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 / Formation of the beta-catenin:TCF transactivating 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 / PML body / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / regulation of protein stability / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of miRNA transcription / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / RNA-directed DNA polymerase / transcription coactivator binding / specific granule lumen / positive regulation of type II interferon production
Similarity search - Function
: / : / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / : / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : / T-cell receptor alpha chain, constant domain ...: / : / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / : / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / : / 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 / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 22 / T cell receptor beta variable 6-5 / Human nkt tcr alpha chain / Human nkt tcr beta chain / Telomerase reverse transcriptase / 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 / molecular replacement / Resolution: 2.81 Å
AuthorsRizkallah, P.J. / Lloyd, A. / Crowther, M. / Cole, D.K. / Sewell, A.K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Mechanism Underpinning Cross-reactivity of a CD8+ T-cell Clone That Recognizes a Peptide Derived from Human Telomerase Reverse Transcriptase.
Authors: Cole, D.K. / van den Berg, H.A. / Lloyd, A. / Crowther, M.D. / Beck, K. / Ekeruche-Makinde, J. / Miles, J.J. / Bulek, A.M. / Dolton, G. / Schauenburg, A.J. / Wall, A. / Fuller, A. / Clement, ...Authors: Cole, D.K. / van den Berg, H.A. / Lloyd, A. / Crowther, M.D. / Beck, K. / Ekeruche-Makinde, J. / Miles, J.J. / Bulek, A.M. / Dolton, G. / Schauenburg, A.J. / Wall, A. / Fuller, A. / Clement, M. / Laugel, B. / Rizkallah, P.J. / Wooldridge, L. / Sewell, A.K.
History
DepositionNov 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Mar 22, 2017Group: Refinement description
Revision 1.4Jan 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 1.5Nov 13, 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: ILE-LEU-ALA-LYS-PHE-LEU-HIS-TRP-LEU
D: Protein TRAV22,Human nkt tcr alpha chain
E: Protein TRBV6-5,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,97116
Polymers94,0885
Non-polymers88311
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-96 kcal/mol
Surface area37740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.160, 48.690, 118.100
Angle α, β, γ (deg.)90.000, 108.150, 90.000
Int Tables number4
Space group name H-MP1211

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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: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61769
#4: Protein Protein TRAV22,Human nkt tcr alpha chain / Human nkt tcr beta chain


Mass: 22223.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV22, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J277, UniProt: K7N5M3
#5: Protein Protein TRBV6-5,Human nkt tcr beta chain


Mass: 26891.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV6-5, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0K1A5, UniProt: K7N5M4

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide ILE-LEU-ALA-LYS-PHE-LEU-HIS-TRP-LEU


Mass: 1142.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14746*PLUS

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Non-polymers , 4 types, 70 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 54.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulphate, 0.1M HEPES pH7, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.809→56.112 Å / Num. all: 25031 / Num. obs: 25031 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rpim(I) all: 0.072 / Rrim(I) all: 0.142 / Rsym value: 0.1 / Net I/av σ(I): 6.889 / Net I/σ(I): 9.2 / Num. measured all: 91454
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.81-2.883.70.730.9199.8
2.88-2.963.60.5791.2199.8
2.96-3.053.80.4911.4199.8
3.05-3.143.80.3811.8199.9
3.14-3.243.80.3062.2199.8
3.24-3.363.70.2183.2199.4
3.36-3.483.50.1773.9199.6
3.48-3.633.60.1315.4199.7
3.63-3.793.60.1076.6199.8
3.79-3.973.70.0858.3199.9
3.97-4.193.70.06910.3199.8
4.19-4.443.60.05712.6199.7
4.44-4.753.60.05312.7199.6
4.75-5.133.70.05113.31100
5.13-5.623.80.05412.2199.4
5.62-6.283.60.0611.1199.9
6.28-7.253.50.05611.6199.7
7.25-8.883.60.04314199.7
8.88-12.563.40.03616.4199.2
12.56-56.1123.20.03318.5197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 2.81→38.03 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.87 / SU B: 42.321 / SU ML: 0.377 / SU R Cruickshank DPI: 0.3246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 1267 5.1 %RANDOM
Rwork0.1887 ---
obs0.1931 23666 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.15 Å2 / Biso mean: 57.144 Å2 / Biso min: 19.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å2-0 Å20.48 Å2
2---2.57 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.81→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 51 59 6739
Biso mean--75.18 40.07 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196854
X-RAY DIFFRACTIONr_bond_other_d0.0020.026156
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.9299308
X-RAY DIFFRACTIONr_angle_other_deg1.191314162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5165820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20123.897349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.982151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3741546
X-RAY DIFFRACTIONr_chiral_restr0.1290.2982
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217818
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021690
X-RAY DIFFRACTIONr_mcbond_it1.1392.7983295
X-RAY DIFFRACTIONr_mcbond_other1.1392.7973294
X-RAY DIFFRACTIONr_mcangle_it1.9584.1924110
LS refinement shellResolution: 2.811→2.884 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 75 -
Rwork0.352 1753 -
all-1828 -
obs--99.62 %
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)
14.65971.08510.62791.91070.69093.51090.09130.2219-0.013-0.1874-0.02820.1736-0.2358-0.379-0.06310.03880.045-0.01610.16620.00210.023432.15780.0673-12.4584
22.688-1.8179-0.86637.05714.00085.08970.0415-0.26180.640.1311-0.2750.4056-0.6822-0.48180.23350.21280.07190.05370.4724-0.06550.319216.235414.848415.7672
34.7691.4436-1.31342.394-2.60576.71140.1771-0.2973-0.05270.3565-0.136-0.0242-0.0726-0.0097-0.04120.0806-0.0399-0.00270.1288-0.05490.037333.0247-0.011114.8451
40.5839-0.31120.37232.9301-1.35049.16510.02310.24470.0911-0.17110.05630.2811-0.2087-0.9417-0.07940.02320.0602-0.00980.52540.00790.184825.6057-3.698-42.8269
57.8009-0.37210.83963.8114-0.59955.14640.04950.22-0.4633-0.2021-0.01820.02740.2288-0.6136-0.03130.1602-0.05230.03750.6552-0.040.09332.2604-14.0403-73.8063
62.5763-1.2938-0.79425.01093.88526.9023-0.0368-0.0493-0.38730.02170.2029-0.24290.73680.3317-0.16610.13580.0390.0150.28930.03050.166645.3438-15.3906-36.7896
73.1955-1.12880.89544.8617-2.34556.82990.05720.1363-0.2083-0.08150.0883-0.11430.2770.0521-0.14540.0997-0.04370.09770.5184-0.15270.16747.0032-13.0321-66.7123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 200
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 246

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