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- PDB-2bck: Crystal Structure of HLA-A*2402 Complexed with a telomerase peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bck | ||||||
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Title | Crystal Structure of HLA-A*2402 Complexed with a telomerase peptide | ||||||
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![]() | IMMUNE SYSTEM / Immunoglobulin Domains / Beta barrels / MHC Fold | ||||||
Function / homology | ![]() 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 / nuclear telomere cap complex / siRNA processing / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / telomerase RNA binding / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / 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 / RNA-templated transcription / CD8 receptor binding / telomeric DNA binding / 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 Extension By Telomerase / TAP binding / telomere maintenance via telomerase / protection from natural killer cell mediated cytotoxicity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / replicative senescence / positive regulation of Wnt signaling pathway / positive regulation of G1/S transition of mitotic cell cycle / beta-2-microglobulin binding / 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 / mitochondrion organization / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / positive regulation of nitric-oxide synthase activity / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 glucose import / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 protein stability / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / PML body / MHC class I protein complex / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / positive regulation of miRNA transcription / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / RNA-directed DNA polymerase / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of angiogenesis / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Jakobsen, B.K. / Cole, D.K. / Gao, G.F. | ||||||
![]() | ![]() Title: Crystal structure of HLA-A*2402 complexed with a telomerase peptide. Authors: Cole, D.K. / Rizkallah, P.J. / Gao, F. / Watson, N.I. / Boulter, J.M. / Bell, J.I. / Sami, M. / Gao, G.F. / Jakobsen, B.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.2 KB | Display | ![]() |
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PDB format | ![]() | 138.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.2 KB | Display | ![]() |
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Full document | ![]() | 504.1 KB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ao7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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Details | One biological unit is made up of 1 heavy chain, 1 light chain and 1 peptide. There are two copies in the asymmetric unit: Chains A,B and C make one biological unit; Chains D,E and F amke another biological unit |
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Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 33720.203 Da / Num. of mol.: 2 / Fragment: residues 1-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: residues 1-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1028.248 Da / Num. of mol.: 2 / Fragment: residues 1-9 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human. References: UniProt: O14746, RNA-directed DNA polymerase |
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-Non-polymers , 3 types, 140 molecules ![](data/chem/img/SO4.gif)
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 1.6M Ammonium Sulphate, 0.1M Sodium Chloride, 0.1M HEPES, 10% v/v Dioxane, pH 7.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2004 |
Radiation | Monochromator: Si(111) sagittal bend / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→78.62 Å / Num. obs: 28450 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 79.3 Å2 / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible obs: 99.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.917 / Mean I/σ(I) obs: 1.2 / Num. measured obs: 4174 / Num. unique all: 4174 / Rsym value: 0.917 / % possible all: 99.7 |
-Phasing
Phasing MR | Rfactor: 46 / R rigid body: 46.4 / Cor.coef. Fo:Fc: 53.9 / Cor.coef. Io to Ic: 26.1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AO7 Resolution: 2.8→78.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 29.779 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.915 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, BUT NOT OUTPUT TO THE COORDINATE SET
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.865 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→78.57 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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