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- PDB-5mer: Human Leukocyte Antigen A02 presenting ILAKFLHEL -

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Basic information

Entry
Database: PDB / ID: 5mer
TitleHuman Leukocyte Antigen A02 presenting ILAKFLHEL
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • ILE-LEU-ALA-LYS-PHE-LEU-HIS-GLU-LEU
KeywordsIMMUNE SYSTEM / HLA / TCR / cross-reactivity / telomerase / HLA A02
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 / telomerase catalytic core complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase activity ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / telomerase catalytic core complex / positive regulation of protein localization to nucleolus / siRNA transcription / telomerase activity / Regulation of MITF-M-dependent genes involved in DNA damage repair and senescence / : / RNA-templated DNA biosynthetic process / establishment of protein localization to telomere / nuclear telomere cap complex / siRNA processing / telomerase RNA binding / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / DNA biosynthetic process / telomeric DNA binding / CD8 receptor binding / RNA-templated transcription / positive regulation of stem cell proliferation / mitochondrial nucleoid / antigen processing and presentation of exogenous peptide antigen via MHC class I / negative regulation of cellular senescence / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / telomere maintenance via telomerase / Telomere Extension By Telomerase / TAP binding / replicative senescence / protection from natural killer cell mediated cytotoxicity / positive regulation of Wnt signaling pathway / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / beta-2-microglobulin binding / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of endothelial cell apoptotic process / T cell receptor binding / response to cadmium ion / detection of bacterium / positive regulation of vascular associated smooth muscle cell proliferation / telomere maintenance / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / 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 / mitochondrion organization / positive regulation of D-glucose import / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / Formation of the beta-catenin:TCF transactivating complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / regulation of protein stability / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / PML body / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / transcription coactivator binding / positive regulation of miRNA transcription / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / RNA-directed DNA polymerase / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of type II interferon production / positive regulation of angiogenesis / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence
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 / Immunoglobulins / Immunoglobulin-like fold / 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 / molecular replacement / Resolution: 1.88 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 ...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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 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
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: ILE-LEU-ALA-LYS-PHE-LEU-HIS-GLU-LEU
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: ILE-LEU-ALA-LYS-PHE-LEU-HIS-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,17145
Polymers89,8326
Non-polymers3,33939
Water8,179454
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: ILE-LEU-ALA-LYS-PHE-LEU-HIS-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,34820
Polymers44,9163
Non-polymers1,43217
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: ILE-LEU-ALA-LYS-PHE-LEU-HIS-GLU-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,82425
Polymers44,9163
Non-polymers1,90822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.970, 170.280, 45.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODD1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 31951.316 Da / Num. of mol.: 2
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.: 2
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, 2 molecules CF

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


Mass: 1085.338 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) / References: UniProt: O14746*PLUS

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Non-polymers , 6 types, 493 molecules

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


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium sulphate, 0.1M MES pH7, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.88→34.06 Å / Num. obs: 76630 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.044 / Net I/σ(I): 10.8 / Num. measured all: 545975
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.88-1.937.60.6663.20.9131100
8.41-34.066.30.04722.10.998198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.16 Å33.35 Å
Translation6.16 Å33.35 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I4W

4i4w


Resolution: 1.88→34.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.682 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 3797 5 %RANDOM
Rwork0.1844 ---
obs0.1863 72747 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 119.82 Å2 / Biso mean: 33.021 Å2 / Biso min: 12.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.88→34.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 198 454 6988
Biso mean--57.4 39.98 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196737
X-RAY DIFFRACTIONr_bond_other_d0.0050.026083
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9439105
X-RAY DIFFRACTIONr_angle_other_deg1.21313994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5565774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43123.125352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.113151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7471556
X-RAY DIFFRACTIONr_chiral_restr0.1540.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027500
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021668
X-RAY DIFFRACTIONr_mcbond_it1.5571.5653099
X-RAY DIFFRACTIONr_mcbond_other1.5531.5653098
X-RAY DIFFRACTIONr_mcangle_it2.282.3323872
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A15284
12D15284
21B5728
22E5728
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 274 -
Rwork0.243 5307 -
all-5581 -
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)
12.72780.0487-0.09353.2956-1.18022.290.095-0.1464-0.05380.1336-0.1672-0.23210.02360.31860.07220.013-0.0057-0.01620.07060.00910.066247.127629.071135.734
26.1240.13222.54242.02521.08543.96690.26510.4283-0.5068-0.2744-0.0972-0.05820.2420.0826-0.16780.13830.0201-0.03050.0375-0.03070.054120.22889.109723.3238
34.61982.0955-1.17953.5044-0.70272.02540.1404-0.23630.24320.087-0.07360.1819-0.0702-0.0829-0.06670.0242-0.01750.00130.0335-0.00680.017219.729726.797837.0875
42.54860.14530.15643.41441.15281.97560.0805-0.13670.03230.1082-0.16240.249-0.0023-0.27170.08190.009-0.00770.01590.0528-0.02030.073318.348855.890612.9492
56.01130.5998-2.67421.9343-1.08894.27270.23610.39260.501-0.3053-0.06680.1493-0.1933-0.1088-0.16930.11660.02560.00970.03330.0250.074145.099575.96770.459
64.62552.12071.20593.33840.79861.96360.141-0.2408-0.23670.0972-0.0824-0.17620.08410.1073-0.05870.024-0.01270.00040.03590.00780.017945.716858.320814.2347
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 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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