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基本情報
登録情報 | データベース: PDB / ID: 7yat | ||||||||||||||||||
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タイトル | CryoEM tetra protofilament structure of the hamster prion 108-144 fibril | ||||||||||||||||||
![]() | Major prion protein | ||||||||||||||||||
![]() | PROTEIN FIBRIL / Prion / fibril / hamster | ||||||||||||||||||
機能・相同性 | ![]() aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / cupric ion binding / negative regulation of dendritic spine maintenance / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade ...aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / cupric ion binding / negative regulation of dendritic spine maintenance / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / cellular response to copper ion / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / presynapse / signaling receptor activity / amyloid-beta binding / protease binding / microtubule binding / nuclear membrane / amyloid fibril formation / response to oxidative stress / learning or memory / regulation of cell cycle / intracellular signal transduction / membrane raft / copper ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / identical protein binding / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | ![]() | ||||||||||||||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 2.2 Å | ||||||||||||||||||
![]() | Chen, E.H.-L. / Kao, S.-W. / Lee, C.-H. / Huang, J.Y.C. / Chen, R.P.-Y. / Wu, K.-P. | ||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: 2.2 Å Cryo-EM Tetra-Protofilament Structure of the Hamster Prion 108-144 Fibril Reveals an Ordered Water Channel in the Center. 著者: Eric H-L Chen / Hsi-Wen Kao / Chih-Hsuan Lee / Jessica Y C Huang / Kuen-Phon Wu / Rita P-Y Chen / ![]() 要旨: Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based ...Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based on the gold-standard Fourier shell correlation (FSC) curve. The fibril has a novel architecture that has never been found in other amyloid fibrils. Each fibril is assembled by four protofilaments (PFs) and has an ordered water channel in the center. Each protofilament contains three β-strands (125-130, 133-135, and 138-141) arranged in an "R"-shaped construct. The structural data indicate that these three β-strand segments are the most amyloidogenic region of the prion peptide/protein and might be the site of nucleation during fibrillization under conditions without denaturants. | ||||||||||||||||||
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 95.9 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 1014.9 KB | 表示 | ![]() |
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XML形式データ | ![]() | 28.6 KB | 表示 | |
CIF形式データ | ![]() | 42.9 KB | 表示 | |
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-関連構造データ
関連構造データ | ![]() 33719MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質・ペプチド | 分子量: 2499.955 Da / 分子数: 24 / 由来タイプ: 合成 / 由来: (合成) ![]() #2: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
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試料調製
構成要素 | 名称: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center タイプ: TISSUE / Entity ID: #1 / 由来: SYNTHETIC |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
緩衝液 | pH: 3.7 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: TFS KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 1 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: -1.76 ° / 軸方向距離/サブユニット: 4.77 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 2368403 | ||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 336759 / 対称性のタイプ: HELICAL | ||||||||||||||||||||||||||||
原子モデル構築 | B value: 21.9 / プロトコル: AB INITIO MODEL / 空間: REAL |