- PDB-4ril: Structure of the amyloid forming segment, GAVVTGVTAVA, from the N... -
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Basic information
Entry
Database: PDB / ID: 4ril
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
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.
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.
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Components
#1: Protein/peptide
Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP
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
Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 4
EM experiment
Aggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography
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Sample preparation
Component
Name: amyloid forming segment GAVVTGVTAVA from the NAC domain of alpha-synuclein Type: COMPLEX
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
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