+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4np8 | |||||||||
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タイトル | Structure of an amyloid forming peptide VQIVYK from the second repeat region of tau (alternate polymorph) | |||||||||
要素 | Microtubule-associated protein tau | |||||||||
キーワード | PROTEIN FIBRIL / amyloid-like protofibril | |||||||||
機能・相同性 | 機能・相同性情報 plus-end-directed organelle transport along microtubule / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / axonal transport / 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 / negative regulation of kinase activity / regulation of long-term synaptic depression / negative regulation of tubulin deacetylation / generation of neurons / rRNA metabolic process / internal protein amino acid acetylation / regulation of chromosome organization / regulation of mitochondrial fission / axonal transport of mitochondrion / intracellular distribution of mitochondria / axon development / central nervous system neuron development / regulation of microtubule polymerization / apolipoprotein binding / microtubule polymerization / lipoprotein particle binding / minor groove of adenine-thymine-rich DNA binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / protein polymerization / axolemma / negative regulation of mitochondrial fission / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / regulation of cellular response to heat / positive regulation of protein localization / cytoplasmic microtubule organization / stress granule assembly / supramolecular fiber organization / regulation of calcium-mediated signaling / axon cytoplasm / somatodendritic compartment / positive regulation of microtubule polymerization / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / 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 / microglial cell activation / synapse organization / Hsp90 protein binding / protein homooligomerization / PKR-mediated signaling / regulation of synaptic plasticity / : / memory / SH3 domain binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / microtubule cytoskeleton / neuron projection development / cell-cell signaling / single-stranded DNA binding / protein-folding chaperone binding / actin binding / protein-macromolecule adaptor activity / cellular response to heat / double-stranded DNA binding / growth cone / cell body / microtubule binding / microtubule / sequence-specific DNA binding / amyloid fibril formation / 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 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.51 Å | |||||||||
データ登録者 | Landau, M. / Eisenberg, D. / Sawaya, M.R. / Dannenberg, J. / Kobko, N. | |||||||||
引用 | ジャーナル: Nat.Struct.Mol.Biol. / 年: 2009 タイトル: Molecular mechanisms for protein-encoded inheritance. 著者: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D. | |||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4np8.cif.gz | 9.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4np8.ent.gz | 5.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4np8.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 4np8_validation.pdf.gz | 372.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4np8_full_validation.pdf.gz | 372.6 KB | 表示 | |
XML形式データ | 4np8_validation.xml.gz | 2.3 KB | 表示 | |
CIF形式データ | 4np8_validation.cif.gz | 2.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/np/4np8 ftp://data.pdbj.org/pub/pdb/validation_reports/np/4np8 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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詳細 | The biological unit is a pair of beta 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 -1/2-X,1/2+Y,-Z; -1/2-X,3/2+Y,-Z; -1/2-X,5/2+Y,-Z; 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: UNP residues 623-628 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P10636 |
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#2: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 1.56 Å3/Da / 溶媒含有率: 21.29 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: reservoir contained 14% iso-Propanol, 0.07M HEPES-Na pH 7.5, 0.14M Sodium Citrate, and 30% Glycerol, vapor diffusion, hanging drop, temperature 298K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.9792 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年2月25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: 1.5→90 Å / Num. all: 825 / Num. obs: 825 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / 冗長度: 4.1 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.1 |
反射 シェル | 解像度: 1.5→1.62 Å / 冗長度: 4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.7 / Num. unique all: 156 / % possible all: 82.1 |
-位相決定
位相決定 | 手法: 分子置換 |
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-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 2ON9 解像度: 1.51→16.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8187 / SU B: 1.895 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0982 / SU Rfree: 0.0894 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.089 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 1.2 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 26.57 Å2 / Biso mean: 7.5741 Å2 / Biso min: 3.8 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.51→16.78 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.508→1.547 Å / Total num. of bins used: 20
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