[English] 日本語
Yorodumi- PDB-5men: Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5men | ||||||
---|---|---|---|---|---|---|---|
Title | Human Leukocyte Antigen A02 presenting ILAKFLHWL, in complex with cognate T-Cell Receptor | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity | ||||||
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 / 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 / T cell receptor complex / 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 / response to bacterium / 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 / multicellular organismal-level iron ion homeostasis / transcription coactivator binding / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 Å | ||||||
Authors | Rizkallah, P.J. / Lloyd, A. / Crowther, M. / Cole, D.K. / Sewell, A.K. | ||||||
Citation | Journal: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5men.cif.gz | 351.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5men.ent.gz | 286 KB | Display | PDB format |
PDBx/mmJSON format | 5men.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5men_validation.pdf.gz | 500.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5men_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 5men_validation.xml.gz | 31.7 KB | Display | |
Data in CIF | 5men_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/5men ftp://data.pdbj.org/pub/pdb/validation_reports/me/5men | HTTPS FTP |
-Related structure data
Related structure data | 5meoC 5mepC 5meqC 5merC 4i4wS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 4 types, 4 molecules ABDE
#1: Protein | 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 | 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 | 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 | 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 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1142.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14746*PLUS |
---|
-Non-polymers , 4 types, 70 molecules
#6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-SO4 / #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.53 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium sulphate, 0.1M HEPES pH7, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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 |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.15 Å2 / Biso mean: 57.144 Å2 / Biso min: 19.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.81→38.03 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.811→2.884 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|