+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3ktm | ||||||
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タイトル | Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP) | ||||||
要素 | Amyloid beta A4 protein | ||||||
キーワード | CELL ADHESION / SIGNALING PROTEIN / Protein Structure / Alzheimer disease / Amyloid / Amyloidosis / Apoptosis / Copper / Disease mutation / Disulfide bond / Endocytosis / Heparin-binding / Metal-binding / Neurodegeneration / Notch signaling pathway / Proteoglycan / Zinc | ||||||
機能・相同性 | 機能・相同性情報 regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity ...regulation of epidermal growth factor-activated receptor activity / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / regulation of synapse structure or activity / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / synaptic assembly at neuromuscular junction / signaling receptor activator activity / smooth endoplasmic reticulum calcium ion homeostasis / axon midline choice point recognition / 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 / positive regulation of amyloid fibril formation / neuron remodeling / : / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / suckling behavior / nuclear envelope lumen / dendrite development / COPII-coated ER to Golgi transport vesicle / presynaptic active zone / modulation of excitatory postsynaptic potential / 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 / intracellular copper ion homeostasis / negative regulation of neuron differentiation / ECM proteoglycans / smooth endoplasmic reticulum / positive regulation of T cell migration / spindle midzone / Purinergic signaling in leishmaniasis infection / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / positive regulation of chemokine production / clathrin-coated pit / regulation of peptidyl-tyrosine phosphorylation / forebrain development / Notch signaling pathway / Mitochondrial protein degradation / neuron projection maintenance / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of protein metabolic process / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / cholesterol metabolic process / positive regulation of mitotic cell cycle / response to interleukin-1 / adult locomotory behavior / extracellular matrix organization / axonogenesis / platelet alpha granule lumen / trans-Golgi network membrane / positive regulation of peptidyl-threonine phosphorylation / dendritic shaft / learning / positive regulation of interleukin-1 beta production / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / endosome lumen / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / synapse organization / regulation of long-term neuronal synaptic plasticity / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / visual learning / serine-type endopeptidase inhibitor activity / neuromuscular junction / recycling endosome / cognition / neuron cellular homeostasis / Golgi lumen / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / endocytosis / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / neuron projection development / cell-cell junction / synaptic vesicle 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: 2.7 Å | ||||||
データ登録者 | Dahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2010 タイトル: Structure and biochemical analysis of the heparin-induced E1 dimer of the amyloid precursor protein. 著者: Dahms, S.O. / Hoefgen, S. / Roeser, D. / Schlott, B. / Guhrs, K.H. / Than, M.E. | ||||||
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 | 3ktm.cif.gz | 292.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3ktm.ent.gz | 237.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3ktm.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 | 3ktm_validation.pdf.gz | 549.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3ktm_full_validation.pdf.gz | 584.3 KB | 表示 | |
XML形式データ | 3ktm_validation.xml.gz | 57.7 KB | 表示 | |
CIF形式データ | 3ktm_validation.cif.gz | 77.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/kt/3ktm ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3ktm | HTTPS FTP |
-関連構造データ
-リンク
-集合体
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 21762.080 Da / 分子数: 8 / 断片: UNP residues 18-190 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: APP, A4, AD1 / プラスミド: pET22b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Origami B(DE3) / 参照: UniProt: P05067 #2: 化合物 | ChemComp-BU4 / ( #3: 化合物 | ChemComp-SO4 / #4: 化合物 | ChemComp-ACT / #5: 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: 4.02 Å3/Da / 溶媒含有率: 69.44 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5 詳細: pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: BESSY / ビームライン: 14.1 / 波長: 0.91841 Å |
検出器 | タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2008年12月19日 / 詳細: Double crystal monochromator with 2 sets of mirrors |
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: 0.91841 Å / 相対比: 1 |
反射 | 解像度: 2.7→29 Å / Num. obs: 74422 / % possible obs: 99.8 % / 冗長度: 2.1 % / Biso Wilson estimate: 69.152 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.8 |
反射 シェル | 解像度: 2.7→2.85 Å / % possible obs: 99.7 % / 冗長度: 2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10822 |
-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: 1MWP, 2FJZ 解像度: 2.7→29 Å
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原子変位パラメータ | Biso mean: 48.6 Å2 | ||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.7→29 Å
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拘束条件 |
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