+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-3001 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | MicroED structure of the segment, GVVHGVTTVA, from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56 | |||||||||
![]() | 2mFo-dFc map covering multiple unit cells. Structure factors measured from micro electron diffraction (microED) methods. | |||||||||
![]() |
| |||||||||
![]() | Amyloid fibrils / alpha-synuclein / MicroED Crystallography / Parkinson's Disease / Peptide / familial mutation A53T | |||||||||
機能・相同性 | ![]() 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 / 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 / synaptic vesicle transport / dopamine uptake involved in synaptic transmission / dynein complex binding / regulation of dopamine secretion / positive regulation of receptor recycling / 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 / kinesin binding / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / adult locomotory behavior / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / microglial cell activation / negative regulation of protein kinase activity / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / tau protein binding / positive regulation of protein serine/threonine kinase activity / PKR-mediated signaling / 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 / cellular response to oxidative stress / histone binding / cell cortex / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / oxidoreductase activity / lysosome / transcription cis-regulatory region binding / response to xenobiotic stimulus 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 電子線結晶学 / クライオ電子顕微鏡法 / 解像度: 1.4 Å | |||||||||
![]() | Rodriguez JA / Ivanova M / Sawaya MR / Cascio D / Reyes F / Shi D / Johnson L / Guenther E / Sangwan S / Hattne J ...Rodriguez JA / Ivanova M / Sawaya MR / Cascio D / Reyes F / Shi D / Johnson L / Guenther E / Sangwan S / Hattne J / Nannenga B / Gonen T / Eisenberg D | |||||||||
![]() | ![]() タイトル: Structure of the toxic core of α-synuclein from invisible crystals. 著者: 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 ...著者: 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 / ![]() 要旨: 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. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
-
ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 263.8 KB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 12.2 KB 12.2 KB | 表示 表示 | ![]() |
画像 | ![]() | 399 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | 2mFo-dFc map covering multiple unit cells. Structure factors measured from micro electron diffraction (microED) methods. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X: 0.44825 Å / Y: 0.3925 Å / Z: 0.45875 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-
試料の構成要素
-全体 : GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson'...
全体 | 名称: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56 |
---|---|
要素 |
|
-超分子 #1000: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson'...
超分子 | 名称: GVVHGVTTVA, a segment from the A53T familial mutant of Parkinson's disease protein, alpha-synuclein, residues 47-56 タイプ: sample / ID: 1000 / 詳細: crystalline fibrils / 集合状態: crystalline fibrils / Number unique components: 1 |
---|
-分子 #1: alpha synuclein residues 47-56
分子 | 名称: alpha synuclein residues 47-56 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: a-syn 詳細: alpha synuclein residues 47-56 with A53T mutation. Synthesized chemically. コピー数: 1 / 集合状態: fibril / 組換発現: No / データベース: NCBI |
---|---|
由来(天然) | 生物種: ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 電子線結晶学 |
試料の集合状態 | 3D array |
-
試料調製
濃度 | 5 mg/mL |
---|---|
緩衝液 | pH: 7 / 詳細: 50 mM phosphate, 0.1% w/v DMSO |
グリッド | 詳細: quantifoil holey-carbon EM grid, 300 mesh copper |
凍結 | 凍結剤: ETHANE / チャンバー内温度: 100 K / 装置: FEI VITROBOT MARK IV 手法: Nanocrystals were deposited onto a quantifoil holey-carbon EM grid in a 2-3 microliter drop after appropriate dilution, which optimized for crystal density on the grid. All grids were then ...手法: Nanocrystals were deposited onto a quantifoil holey-carbon EM grid in a 2-3 microliter drop after appropriate dilution, which optimized for crystal density on the grid. All grids were then blotted and vitrified by plunging into liquid ethane using a Vitrobot Mark IV (FEI), then transferring to liquid nitrogen for storage. |
詳細 | Crystals grew in batch. In a microcentrifuge tube at 37 degrees C with shaking. |
結晶化 | 詳細: Crystals grew in batch. In a microcentrifuge tube at 37 degrees C with shaking. |
-
電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
---|---|
温度 | 最低: 99 K / 最高: 101 K / 平均: 100 K |
詳細 | very low dose data collection. Spot size 11. |
日付 | 2015年4月20日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) 実像数: 343 / 平均電子線量: 0.10000000000000001 e/Å2 / カメラ長: 2230 / 詳細: Diffraction images are available upon request. / ビット/ピクセル: 16 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | 照射モード: OTHER / 撮影モード: DIFFRACTION |
試料ステージ | 試料ホルダー: liquid nitrogen cooled / 試料ホルダーモデル: GATAN LIQUID NITROGEN / Tilt angle min: -66 / Tilt angle max: 66 / Tilt series - Axis1 - Min angle: -66 ° / Tilt series - Axis1 - Max angle: 66 ° |
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
-
画像解析
詳細 | Diffraction images were processed with XDS and XSCALE. Please note that the unit cell length B is 4.71 A. This value was not accepted as valid on the web submission page. |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 1.4 Å / 解像度の算出法: DIFFRACTION PATTERN/LAYERLINES 詳細: The diffraction data set contains intensities measured from three crystals. |
結晶パラメータ | 単位格子 - A: 17.930 Å / 単位格子 - B: 4.71 Å / 単位格子 - C: 33.030 Å / 単位格子 - γ: 90.0 ° / 単位格子 - α: 90 ° / 単位格子 - β: 94.33 ° / 空間群: P 1 21 1 |