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Yorodumi- PDB-4r0u: Tgvtava, an amyloid forming segment from alpha synuclein, residue... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r0u | ||||||
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Title | Tgvtava, an amyloid forming segment from alpha synuclein, residues 72-78 | ||||||
Components | Alpha-synuclein | ||||||
Keywords | PROTEIN FIBRIL / amyloid-like protofibril | ||||||
Function / homology | Function and homology information negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / dopamine biosynthetic process / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine uptake involved in synaptic transmission / regulation of locomotion / synaptic vesicle priming / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / mitochondrial ATP synthesis coupled electron transport / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / kinesin binding / regulation of presynapse assembly / alpha-tubulin binding / synaptic vesicle endocytosis / negative regulation of serotonin uptake / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / cellular response to epinephrine stimulus / excitatory postsynaptic potential / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / regulation of transmembrane transporter activity / ferrous iron binding / protein tetramerization / synapse organization / phosphoprotein binding / regulation of long-term neuronal synaptic plasticity / microglial cell activation / negative regulation of protein kinase activity / phospholipid binding / protein destabilization / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / positive regulation of protein serine/threonine kinase activity / receptor internalization / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / actin binding / cell cortex / growth cone / histone binding / chemical synaptic transmission / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / lysosome / oxidoreductase activity / molecular adaptor activity / transcription cis-regulatory region binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å | ||||||
Authors | Ivanova, M.I. / Eisenberg, D.S. / Sawaya, M.R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Structure-based design of functional amyloid materials. Authors: Li, D. / Jones, E.M. / Sawaya, M.R. / Furukawa, H. / Luo, F. / Ivanova, M. / Sievers, S.A. / Wang, W. / Yaghi, O.M. / Liu, C. / Eisenberg, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r0u.cif.gz | 8.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r0u.ent.gz | 5.3 KB | Display | PDB format |
PDBx/mmJSON format | 4r0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/4r0u ftp://data.pdbj.org/pub/pdb/validation_reports/r0/4r0u | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | There are two choices of the biological unit. The first choice is a pair of indefinitely long beta sheets constructed from chain A and unit cell translations along the b direction (that is, the b direction corresponds to the fiber axis) (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from 1-X,Y+1/2,1-Z and its unit cell translations along the b direction (i.e. 1-x,y+3/2,1-z; 1-x,y+5/2,1-z, etc.). The second choice of biological unit is a pair of beta sheets constructed from chain A and unit cell translations along the b direction (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from -X,1/2+Y,1-Z and its unit cell translations along the b direction (i.e. -x,y+3/2,1-z; -x,y+5/2,1-z; etc.). REMARK 350 displays 5 strands from both sheets for the first choice. |
-Components
#1: Protein/peptide | Mass: 617.692 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-78 / Source method: obtained synthetically Details: TGVTAVA (residues 72-78) from Human alpha-synuclein, synthesized Source: (synth.) Homo sapiens (human) / References: UniProt: P37840 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.52 Å3/Da / Density % sol: 19.34 % / Mosaicity: 0.6 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2M magnesium formate, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.895432 Å | ||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2007 | ||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.895432 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.38→90 Å / Num. all: 798 / Num. obs: 798 / % possible obs: 83.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.151 / Χ2: 1.125 / Net I/σ(I): 8.4 | ||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ideal beta strand Resolution: 1.38→25.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.2528 / WRfactor Rwork: 0.2378 / FOM work R set: 0.7067 / SU B: 2.336 / SU ML: 0.077 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.0873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.77 Å2 / Biso mean: 16.624 Å2 / Biso min: 8.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→25.49 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.38→1.542 Å / Total num. of bins used: 5
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