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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 / detection of bacterium / cellular response to epidermal growth factor stimulus / cellular response to transforming growth factor beta stimulus / regulation of mRNA stability / ERK1 and ERK2 cascade / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / 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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / defense response / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / response to wounding / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / cellular response to tumor necrosis factor / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / ribonucleoprotein complex / immune response / Amyloid fiber formation 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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