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- PDB-5meo: Human Leukocyte Antigen presenting ILGKFLHRL -

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Basic information

Entry
Database: PDB / ID: 5meo
TitleHuman Leukocyte Antigen presenting ILGKFLHRL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • ILE-LEU-GLY-LYS-PHE-LEU-HIS-ARG-LEU
KeywordsIMMUNE SYSTEM / HLA-A02 / HLAA / Telomerase
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / nuclear telomere cap complex / telomere maintenance via recombination / siRNA processing / 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 / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / RNA-templated transcription / DNA biosynthetic process / telomeric DNA binding / positive regulation of stem cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / mitochondrial nucleoid / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of cellular senescence / Telomere Extension By Telomerase / replicative senescence / positive regulation of Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / positive regulation of G1/S transition of mitotic cell cycle / telomere maintenance via telomerase / RNA-directed DNA polymerase activity / negative regulation of endothelial cell apoptotic process / detection of bacterium / T cell receptor binding / response to cadmium ion / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of nitric-oxide synthase activity / : / : / 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 / lumenal side of endoplasmic reticulum membrane / positive regulation of D-glucose import / 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 / cellular response to iron(III) ion / 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 / Formation of the beta-catenin:TCF transactivating complex / 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 / transcription coactivator binding / HFE-transferrin receptor complex / T cell mediated cytotoxicity / regulation of protein stability / antigen processing and presentation of endogenous peptide antigen via MHC class I / PML body / 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 / positive regulation of miRNA transcription / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / RNA-directed DNA polymerase / positive regulation of type II interferon production / telomerase activity
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 / 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 ...: / 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 / 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 / : / 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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
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: 1.772 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 1.3Jan 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 1.4Nov 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
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: ILE-LEU-GLY-LYS-PHE-LEU-HIS-ARG-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,42224
Polymers44,9303
Non-polymers1,49221
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint7 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.200, 74.870, 125.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#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 (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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide ILE-LEU-GLY-LYS-PHE-LEU-HIS-ARG-LEU


Mass: 1099.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: O14746*PLUS

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Non-polymers , 4 types, 368 molecules

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


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate, 0.1 M Tris pH 7.5, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.772→49.2 Å / Num. all: 46011 / Num. obs: 46011 / % possible obs: 100 % / Redundancy: 7.2 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.12 / Rsym value: 0.105 / Net I/av σ(I): 5.126 / Net I/σ(I): 10.5 / Num. measured all: 332927
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.772-1.826.70.71811100
1.82-1.876.80.571.3199.9
1.87-1.926.90.451.61100
1.92-1.9870.3492.11100
1.98-2.057.10.2762.61100
2.05-2.127.30.2313.11100
2.12-2.27.40.2053.51100
2.2-2.297.50.18241100
2.29-2.397.60.1654.41100
2.39-2.517.60.1484.81100
2.51-2.647.60.1355.31100
2.64-2.87.60.1185.91100
2.8-37.50.1076.41100
3-3.247.40.09671100
3.24-3.547.30.0877.6199.9
3.54-3.9670.0778.4199.8
3.96-4.587.60.0679.91100
4.58-5.67.50.0610.61100
5.6-7.937.40.05711.71100
7.936.50.04613.7198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.77 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.16 Å
Translation2.5 Å48.16 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.1.4phasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 1.772→48.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.14 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 2319 5 %RANDOM
Rwork0.1707 ---
obs0.1729 43626 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.27 Å2 / Biso mean: 27.731 Å2 / Biso min: 10.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å20 Å2
2--0.98 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.772→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 94 347 3610
Biso mean--44.79 34.47 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193365
X-RAY DIFFRACTIONr_bond_other_d0.0030.023071
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.9374534
X-RAY DIFFRACTIONr_angle_other_deg1.10137057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6475393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21523.029175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1515539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5721529
X-RAY DIFFRACTIONr_chiral_restr0.1250.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023759
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02838
X-RAY DIFFRACTIONr_mcbond_it0.6931.1531552
X-RAY DIFFRACTIONr_mcbond_other0.6931.1531551
X-RAY DIFFRACTIONr_mcangle_it1.0961.7261938
LS refinement shellResolution: 1.772→1.818 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 166 -
Rwork0.261 3193 -
all-3359 -
obs--100 %
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)
11.73480.6887-0.1142.1963-0.30581.9716-0.0105-0.1040.23830.06880.0052-0.0371-0.31330.02140.00540.08930.0111-0.0090.0113-0.01810.041920.7811-1.60868.2723
22.6312-0.32931.76592.08450.24214.5985-0.027-0.17920.2083-0.0319-0.0660.318-0.2091-0.68160.0930.1420.03190.01570.23350.06230.12065.99686.6456-23.4421
32.19270.001-1.22131.4269-0.68544.3291-0.00320.32510.0062-0.24690.0004-0.010.24130.08510.00280.0828-0.0028-0.01780.09140.01920.018420.8735-9.5428-17.9792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99

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