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Yorodumi- PDB-1w0w: Crystal Structure Of HLA-B*2709 Complexed With the self-Peptide T... -
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-Basic information
Entry | Database: PDB / ID: 1w0w | ||||||
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Title | Crystal Structure Of HLA-B*2709 Complexed With the self-Peptide TIS from EGF-response factor 1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / MAJOR HISTOCOMPATIBILITY COMPLEX / HLA- B*2705 / MHC I | ||||||
Function / homology | Function and homology information negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / negative regulation of stem cell differentiation / M-decay: degradation of maternal mRNAs by maternally stored factors / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / negative regulation of stem cell differentiation / M-decay: degradation of maternal mRNAs by maternally stored factors / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of interleukin-12 production / regulation of dendritic cell differentiation / definitive hemopoiesis / cellular response to fibroblast growth factor stimulus / regulation of T cell anergy / cellular response to glucocorticoid stimulus / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of interleukin-6 production / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / negative regulation of fat cell differentiation / mRNA catabolic process / somatic stem cell population maintenance / hemopoiesis / TAP binding / protection from natural killer cell mediated cytotoxicity / cellular response to epidermal growth factor stimulus / ERK1 and ERK2 cascade / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to transforming growth factor beta stimulus / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / regulation of mRNA stability / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / response to wounding / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / regulation of translation / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / cellular response to tumor necrosis factor / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / ribonucleoprotein complex Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Thermodynamic and Structural Equivalence of Two Hla-B27 Subtypes Complexed with a Self-Peptide Authors: Hulsmeyer, M. / Welfle, K. / Pohlmann, T. / Misselwitz, R. / Alexiev, U. / Welfle, H. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A. #1: Journal: J.Exp.Med. / Year: 2004 Title: Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide Authors: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #2: Journal: J.Biol.Chem. / Year: 2004 Title: Thermodynamic and Structural Analysis of Peptide- and Allele-Dependent Properties of Two Hla-B27 Subtypes Exhibiting Differential Disease Association Authors: Hillig, R.C. / Hulsmeyer, M. / Saenger, W. / Welfle, K. / Misselwitz, R. / Welfle, H. / Kozerski, C. / Volz, A. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w0w.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w0w.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 1w0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/1w0w ftp://data.pdbj.org/pub/pdb/validation_reports/w0/1w0w | HTTPS FTP |
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-Related structure data
Related structure data | 1w0vSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS | ||||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 1160.436 Da / Num. of mol.: 1 / Fragment: RESIDUES 479-487 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P47974 | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | BETA-2-MICROGLOBULIN IS THE BETA-CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES. ...BETA-2-MICROGLOBU | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53 % |
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Crystal grow | pH: 8.5 / Details: 20% PEG8000, 0.1M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.886 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→28.1 Å / Num. obs: 22935 / % possible obs: 87 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.11→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W0V Resolution: 2.11→65.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.551 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→65.94 Å
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Refine LS restraints |
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