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Yorodumi- PDB-4z77: Weak TCR binding to an unstable insulin epitope drives type 1 diabetes -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z77 | ||||||
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Title | Weak TCR binding to an unstable insulin epitope drives type 1 diabetes | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / H-2Kd / Type 1 Diabetes | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / nitric oxide-cGMP-mediated signaling ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / nitric oxide-cGMP-mediated signaling / positive regulation of peptide hormone secretion / antigen processing and presentation of exogenous peptide antigen via MHC class I / positive regulation of respiratory burst / Regulation of gene expression in beta cells / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / beta-2-microglobulin binding / fatty acid homeostasis / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling 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 / positive regulation of mitotic nuclear division / 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 / positive regulation of long-term synaptic potentiation / Regulation of insulin secretion / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / positive regulation of nitric-oxide synthase activity / positive regulation of cell differentiation / Endosomal/Vacuolar pathway / regulation of transmembrane transporter activity / positive regulation of glucose import / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / negative regulation of proteolysis / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / regulation of synaptic plasticity / negative regulation of forebrain neuron differentiation / wound healing / insulin receptor binding / 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 / hormone activity / negative regulation of protein catabolic process / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / cognition / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of neuron projection development / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Model details | G9V in H-2Kd, Monoclinic form | ||||||
Authors | Rizkallah, P.J. / Cole, D.K. | ||||||
Citation | Journal: To Be Published Title: Weak TCR binding to an unstable insulin epitope drives type 1 diabetes Authors: Rizkallah, P.J. / Cole, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z77.cif.gz | 340.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z77.ent.gz | 286.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/4z77 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/4z77 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 32353.016 Da / Num. of mol.: 2 / Fragment: UNP residues 22-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P01902 #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1052.269 Da / Num. of mol.: 2 / Fragment: UNP residues 39-47 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: synthetic construct (others) / References: UniProt: P01308 |
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-Non-polymers , 5 types, 439 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-SO4 / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris propane pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→37.099 Å / Num. all: 64020 / Num. obs: 64020 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rpim(I) all: 0.151 / Rrim(I) all: 0.298 / Rsym value: 0.214 / Net I/av σ(I): 2.133 / Net I/σ(I): 11.7 / Num. measured all: 237464 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 50.43 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→37.099 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.182 / FOM work R set: 0.7798 / SU B: 10.488 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1925 / SU Rfree: 0.1699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.25 Å2 / Biso mean: 28.972 Å2 / Biso min: 8.25 Å2
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Refinement step | Cycle: final / Resolution: 1.85→37.099 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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