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- PDB-5meq: Human Leukocyte Antigen A02 presenting ILAKFLHTL -

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Basic information

Entry
Database: PDB / ID: 5meq
TitleHuman Leukocyte Antigen A02 presenting ILAKFLHTL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • ILE-LEU-ALA-LYS-PHE-LEU-HIS-THR-LEU
KeywordsIMMUNE SYSTEM / HLA / HLA A02 / Immuno / 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 / 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 / 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 / nuclear telomere cap complex / siRNA processing / 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 / RNA-templated transcription / telomeric DNA binding / CD8 receptor 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 / 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 / Telomere Extension By Telomerase / 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 Wnt signaling pathway / 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 protein binding / telomere maintenance via telomerase / detection of bacterium / negative regulation of endothelial cell apoptotic process / 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 / lumenal side of endoplasmic reticulum 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 / 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 / PML body / 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 / regulation of protein stability / 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 / positive regulation of miRNA transcription / RNA-directed DNA polymerase / transcription coactivator binding / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane
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 / Immunoglobulins / DNA/RNA polymerase superfamily / 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 / Resolution: 2.27 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Lloyd, A. / Crowther, M. / 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 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-THR-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0465
Polymers44,8883
Non-polymers1582
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-26 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.340, 81.440, 56.770
Angle α, β, γ (deg.)90.000, 113.530, 90.000
Int Tables number4
Space group name H-MP1211

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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-ALA-LYS-PHE-LEU-HIS-THR-LEU


Mass: 1057.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Synthetic / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O14746*PLUS

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Non-polymers , 3 types, 111 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
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: I04 / Wavelength: 0.97949 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.27→48.9 Å / Num. obs: 20523 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.119 / Net I/σ(I): 12.8
Reflection shellRmerge(I) obs: 0.751 / Rrim(I) all: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 2.27→48.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 19.828 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.252
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 1023 5 %RANDOM
Rwork0.2033 ---
obs0.2065 19484 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 37.722 Å2 / Biso min: 18.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-0 Å2-3.53 Å2
2--0.86 Å2-0 Å2
3---1.02 Å2
Refinement stepCycle: final / Resolution: 2.27→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 9 109 3284
Biso mean--53.05 36.07 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193278
X-RAY DIFFRACTIONr_bond_other_d0.0020.022957
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9234446
X-RAY DIFFRACTIONr_angle_other_deg1.13436796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2695384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40723.029175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.98215535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1651529
X-RAY DIFFRACTIONr_chiral_restr0.1270.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023722
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02831
X-RAY DIFFRACTIONr_mcbond_it0.8451.5971542
X-RAY DIFFRACTIONr_mcbond_other0.8361.5961541
X-RAY DIFFRACTIONr_mcangle_it1.4722.3851924
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 67 -
Rwork0.292 1454 -
all-1521 -
obs--98.89 %
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)
12.2591-0.74370.37943.6521-1.11012.6274-0.08440.03420.0391-0.0170.0196-0.31020.01410.19770.06480.2567-0.01860.01530.0198-0.00550.027624.0302-5.250613.3634
27.77043.26285.08023.08832.58043.86330.26090.0248-0.42080.0146-0.1240.01820.2711-0.1495-0.13690.30230.00310.02610.0561-0.03950.06520.2833-32.65412.4434
34.31941.274-2.49595.4502-3.02765.2511-0.0502-0.15720.18710.28170.22940.4725-0.1677-0.5104-0.17920.26630.0350.050.1028-0.00350.05120.6715-13.351625.3025
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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