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Yorodumi- PDB-4ril: Structure of the amyloid forming segment, GAVVTGVTAVA, from the N... -
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-Basic information
Entry | Database: PDB / ID: 4ril | ||||||
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Title | Structure of the amyloid forming segment, GAVVTGVTAVA, from the NAC domain of Parkinson's disease protein alpha-synuclein, residues 68-78, determined by electron diffraction | ||||||
Components | Alpha-synuclein | ||||||
Keywords | LIPID BINDING PROTEIN / Amyloid / alpha-synuclein / Parkinson's Disease / Toxic Core / NACore | ||||||
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 / regulation of norepinephrine uptake / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / 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 / synaptic vesicle exocytosis / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / alpha-tubulin binding / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / 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 / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / protein destabilization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / ferrous iron binding / tau protein binding / PKR-mediated signaling / positive regulation of protein serine/threonine kinase activity / receptor internalization / phospholipid binding / 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 / actin binding / cell cortex / cellular response to oxidative stress / histone binding / growth cone / postsynapse / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / transcription cis-regulatory region binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / molecular replacement / cryo EM / Resolution: 1.43 Å | ||||||
Authors | Rodriguez, J.A. / Ivanova, M. / Sawaya, M.R. / Cascio, D. / Reyes, F. / Shi, D. / Johnson, L. / Guenther, E. / Sangwan, S. / Hattne, J. ...Rodriguez, J.A. / Ivanova, M. / Sawaya, M.R. / Cascio, D. / Reyes, F. / Shi, D. / Johnson, L. / Guenther, E. / Sangwan, S. / Hattne, J. / Nannenga, B. / Brewster, A.S. / Messerschmidt, M. / Boutet, S. / Sauter, N.K. / Gonen, T. / Eisenberg, D.S. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Structure of the toxic core of α-synuclein from invisible crystals. Authors: Jose A Rodriguez / Magdalena I Ivanova / Michael R Sawaya / Duilio Cascio / Francis E Reyes / Dan Shi / Smriti Sangwan / Elizabeth L Guenther / Lisa M Johnson / Meng Zhang / Lin Jiang / Mark ...Authors: Jose A Rodriguez / Magdalena I Ivanova / Michael R Sawaya / Duilio Cascio / Francis E Reyes / Dan Shi / Smriti Sangwan / Elizabeth L Guenther / Lisa M Johnson / Meng Zhang / Lin Jiang / Mark A Arbing / Brent L Nannenga / Johan Hattne / Julian Whitelegge / Aaron S Brewster / Marc Messerschmidt / Sébastien Boutet / Nicholas K Sauter / Tamir Gonen / David S Eisenberg / Abstract: The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term ...The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4ril.cif.gz | 10.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ril.ent.gz | 5.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ril.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ril_validation.pdf.gz | 562 KB | Display | wwPDB validaton report |
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Full document | 4ril_full_validation.pdf.gz | 561.6 KB | Display | |
Data in XML | 4ril_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 4ril_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/4ril ftp://data.pdbj.org/pub/pdb/validation_reports/ri/4ril | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a pair of beta-sheets. One sheet is composed of chain A and unit cell translations along the b dimension. The other sheet is composed of the symmetry mate -x+1/2,y+1/2,-z, and unit cell translations along b. |
-Components
#1: Protein/peptide | Mass: 944.083 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic peptide GAVVTGVTAVA corresponding to segment 68-78 of human alpha-synuclein Source: (synth.) Homo sapiens (human) / References: UniProt: P37840 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 4 |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography |
-Sample preparation
Component | Name: amyloid forming segment GAVVTGVTAVA from the NAC domain of alpha-synuclein Type: COMPLEX |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
Crystal | Density Matthews: 1.46 Å3/Da / Density % sol: 15.81 % |
Crystal grow | Temperature: 310 K / Method: batch crystallization / pH: 4 Details: 1 mg of synthetic peptide GAVVTGVTAVA was dissolved in 1 ml of sterile water and shaken overnight in an orbital mixing plate, pH 4.0, batch crystallization, temperature 310K |
-Data collection
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company | |||||||||||||||||||||
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Microscopy | Model: FEI TECNAI F20 | |||||||||||||||||||||
Electron gun | Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM | |||||||||||||||||||||
Electron lens | Mode: DIFFRACTION | |||||||||||||||||||||
Specimen holder | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER | |||||||||||||||||||||
Image recording | Average exposure time: 3.5 sec. / Electron dose: 0.35 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) | |||||||||||||||||||||
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
Diffraction source | Source: ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251 Å | |||||||||||||||||||||
Detector | Type: TVIPS F416 CMOS CAMERA / Detector: CMOS / Date: Aug 28, 2014 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: electron | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.0251 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.43→16.43 Å / Num. all: 1073 / Num. obs: 1073 / % possible obs: 89.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 10.33 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 5.5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4RIK Resolution: 1.43→16.43 Å / Cor.coef. Fo:Fc: 0.9126 / Cor.coef. Fo:Fc free: 0.9002 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso max: 74.5 Å2 / Biso mean: 12.75 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→16.43 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.6 Å / Total num. of bins used: 5
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