+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1x11 | ||||||
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タイトル | X11 PTB DOMAIN | ||||||
要素 |
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キーワード | COMPLEX (PEPTIDE BINDING MODULE/PEPTIDE) / COMPLEX (PEPTIDE BINDING MODULE-PEPTIDE) / PTB DOMAIN / COMPLEX (PEPTIDE BINDING MODULE-PEPTIDE) complex | ||||||
機能・相同性 | 機能・相同性情報 gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / glutamate secretion / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / glutamate secretion / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / Assembly and cell surface presentation of NMDA receptors / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / Neurexins and neuroligins / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of spontaneous synaptic transmission / mating behavior / NMDA selective glutamate receptor signaling pathway / ciliary rootlet / Lysosome Vesicle Biogenesis / PTB domain binding / Golgi-associated vesicle / neuron remodeling / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / positive regulation of G2/M transition of mitotic cell cycle / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / presynaptic active zone / modulation of excitatory postsynaptic potential / regulation of peptidyl-tyrosine phosphorylation / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / neuromuscular process controlling balance / The NLRP3 inflammasome / regulation of presynapse assembly / transition metal ion binding / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / negative regulation of neuron differentiation / ECM proteoglycans / intracellular copper ion homeostasis / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / presynaptic active zone membrane / forebrain development / Notch signaling pathway / neuron projection maintenance / presynaptic modulation of chemical synaptic transmission / positive regulation of protein metabolic process / positive regulation of calcium-mediated signaling / astrocyte activation / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / response to interleukin-1 / cholesterol metabolic process / positive regulation of mitotic cell cycle / extracellular matrix organization / adult locomotory behavior / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-1 beta production / learning / dendritic shaft / positive regulation of long-term synaptic potentiation / Mitochondrial protein degradation / central nervous system development / locomotory behavior / endosome lumen / positive regulation of JNK cascade / Post-translational protein phosphorylation / intracellular protein transport / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / positive regulation of non-canonical NF-kappaB signal transduction / multicellular organism growth / Schaffer collateral - CA1 synapse / recycling endosome / cognition / G2/M transition of mitotic cell cycle / Golgi lumen / positive regulation of inflammatory response / neuron cellular homeostasis 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 多波長異常分散 / 解像度: 2.5 Å | ||||||
データ登録者 | Lee, C.-H. / Zhang, Z. / Kuriyan, J. | ||||||
引用 | ジャーナル: EMBO J. / 年: 1997 タイトル: Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain. 著者: Zhang, Z. / Lee, C.H. / Mandiyan, V. / Borg, J.P. / Margolis, B. / Schlessinger, J. / Kuriyan, J. | ||||||
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 | 1x11.cif.gz | 89.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1x11.ent.gz | 69 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1x11.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 | 1x11_validation.pdf.gz | 423.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1x11_full_validation.pdf.gz | 432 KB | 表示 | |
XML形式データ | 1x11_validation.xml.gz | 8.9 KB | 表示 | |
CIF形式データ | 1x11_validation.cif.gz | 13.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/x1/1x11 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/1x11 | 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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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper: (Code: given Matrix: (0.28, -0.569, 0.773), ベクター: |
-要素
#1: タンパク質 | 分子量: 19801.256 Da / 分子数: 2 / 断片: PTB DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q02410 #2: タンパク質・ペプチド | 分子量: 1637.723 Da / 分子数: 2 / 由来タイプ: 組換発現 / 参照: UniProt: P05067 #3: 水 | ChemComp-HOH / | |
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-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: 2.52 Å3/Da / 溶媒含有率: 51.19 % | ||||||||||||||||||||||||
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結晶化 | pH: 7.5 / 詳細: pH 7.5 | ||||||||||||||||||||||||
結晶化 | *PLUS 温度: 21 ℃ / pH: 6.5 / 手法: 蒸気拡散法, ハンギングドロップ法 | ||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: 回転陽極 / タイプ: RIGAKU RUH2R / 波長: 1.5418 |
検出器 | タイプ: RIGAKU / 検出器: IMAGE PLATE / 日付: 1996年8月1日 / 詳細: MIRRORS |
放射 | 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.4→30 Å / Num. obs: 97157 / % possible obs: 99.3 % / 冗長度: 5.5 % / Rsym value: 0.054 / Net I/σ(I): 27.6 |
反射 シェル | 解像度: 2.4→2.49 Å / Mean I/σ(I) obs: 5.1 / Rsym value: 0.302 / % possible all: 99.2 |
反射 | *PLUS Num. obs: 17790 / Num. measured all: 97157 / Rmerge(I) obs: 0.054 |
反射 シェル | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.302 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 多波長異常分散 / 解像度: 2.5→6 Å / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 詳細: MISSING RESIDUES CORRESPOND TO DISORDERED REGIONS THAT WERE NOT MODELLED.
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原子変位パラメータ | Biso mean: 42.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.5→6 Å
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拘束条件 |
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Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.8 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor all: 0.232 / Rfactor obs: 0.212 / Rfactor Rfree: 0.303 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | *PLUS % reflection Rfree: 10 % |