+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 3ovl | ||||||
---|---|---|---|---|---|---|---|
タイトル | Structure of an amyloid forming peptide VQIVYK from the TAU protein in complex with orange G | ||||||
![]() | Microtubule-associated protein | ||||||
![]() | PROTEIN FIBRIL / amyloid-like protofibril in complex with a small-molecule binder | ||||||
機能・相同性 | ![]() plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / glial cell projection / apolipoprotein binding / negative regulation of mitochondrial membrane potential / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / stress granule assembly / regulation of cellular response to heat / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / microtubule cytoskeleton organization / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / cellular response to heat / single-stranded DNA binding / protein-folding chaperone binding / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding 類似検索 - 分子機能 | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Landau, M. / Eisenberg, D. | ||||||
![]() | ![]() タイトル: Towards a pharmacophore for amyloid. 著者: Landau, M. / Sawaya, M.R. / Faull, K.F. / Laganowsky, A. / Jiang, L. / Sievers, S.A. / Liu, J. / Barrio, J.R. / Eisenberg, D. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 12.2 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 7 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 743.2 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 743.4 KB | 表示 | |
XML形式データ | ![]() | 3.1 KB | 表示 | |
CIF形式データ | ![]() | 3.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 6||||||||
単位格子 |
| ||||||||
Components on special symmetry positions |
| ||||||||
詳細 | The biological unit is a pair of beta sheets with orange G interrelating between two pairs of sheets. One sheet is constructed from chain A and unit cell translations along the b direction (i.e. X,Y+1,Z; X,Y+2,Z; X,Y+3,Z, etc.). The second sheet is constructed from -X-1/2,1/2+Y,-Z;-X-1/2,3/2+Y,-Z;-X-1/2,5/2+Y,-Z; etc. The other pairs of sheets will be contracted from -X,Y,-Z+1, -X,Y+1,-Z+1,-X,Y+2,-Z+1; etc. and from X+1/2,1/2+Y,Z+1, X+1/2,3/2+Y,Z+1, X+1/2,5/2+Y,Z+1; etc. |
-
要素
#1: タンパク質・ペプチド | 分子量: 749.917 Da / 分子数: 1 / 断片: VQIVYK (residues 306-311) / 由来タイプ: 合成 / 詳細: VQIVYK (residues 306-311) from Tau, synthesized / 参照: UniProt: P10636 | ||||||
---|---|---|---|---|---|---|---|
#2: 化合物 | #3: 化合物 | ChemComp-ACY / | #4: 化合物 | ChemComp-ORA / | #5: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 1.91 Å3/Da / 溶媒含有率: 35.66 % |
---|---|
結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: reservoir contained 0.1M Zinc Acetate dihydrate, 18% PEG 3350, vapor diffusion, hanging drop, temperature 291K |
-データ収集
回折 | 平均測定温度: 100 K | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
放射光源 | 由来: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年11月17日 | ||||||||||||||||||||||||||||||||||||||||||
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray | ||||||||||||||||||||||||||||||||||||||||||
放射波長 | 波長: 0.9792 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.8→90 Å / Num. all: 587 / Num. obs: 587 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / 冗長度: 2.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.179 / Χ2: 1.071 / Net I/σ(I): 4.5 | ||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
|
-位相決定
位相決定 | 手法: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 36.92 Å2 / Biso mean: 20.2828 Å2 / Biso min: 6.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.81→26.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 1.805→2.017 Å / Total num. of bins used: 5
|