+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8a00 | ||||||||||||||||||
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タイトル | Infectious mouse-adapted ME7 scrapie prion fibril purified from terminally-infected mouse brains | ||||||||||||||||||
要素 | Major prion protein | ||||||||||||||||||
キーワード | PROTEIN FIBRIL / Prion (プリオン) | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / nucleobase-containing compound metabolic process / response to copper ion / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / activation of protein kinase activity / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / side of membrane / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / 封入体 / cellular response to copper ion / neuron projection maintenance / protein sequestering activity / tubulin binding / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / regulation of protein localization / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / 核膜 / protease binding / response to oxidative stress / mitochondrial outer membrane / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / 脂質ラフト / copper ion binding / intracellular membrane-bounded organelle / 樹状突起 / protein-containing complex binding / negative regulation of apoptotic process / ゴルジ体 / 細胞膜 / 小胞体 / 生体膜 / identical protein binding / metal ion binding / 細胞膜 / 細胞質基質 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||||||||||||||
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: 2.6 Å | ||||||||||||||||||
データ登録者 | Manka, S.W. / Wenborn, A. / Betts, J. / Joiner, S. / Saibil, H.R. / Collinge, J. / Wadsworth, J.D.F. | ||||||||||||||||||
資金援助 | 英国, 5件
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引用 | ジャーナル: Nat Chem Biol / 年: 2023 タイトル: A structural basis for prion strain diversity. 著者: Szymon W Manka / Adam Wenborn / Jemma Betts / Susan Joiner / Helen R Saibil / John Collinge / Jonathan D F Wadsworth / 要旨: Recent cryogenic electron microscopy (cryo-EM) studies of infectious, ex vivo, prion fibrils from hamster 263K and mouse RML prion strains revealed a similar, parallel in-register intermolecular β- ...Recent cryogenic electron microscopy (cryo-EM) studies of infectious, ex vivo, prion fibrils from hamster 263K and mouse RML prion strains revealed a similar, parallel in-register intermolecular β-sheet (PIRIBS) amyloid architecture. Rungs of the fibrils are composed of individual prion protein (PrP) monomers that fold to create distinct N-terminal and C-terminal lobes. However, disparity in the hamster/mouse PrP sequence precludes understanding of how divergent prion strains emerge from an identical PrP substrate. In this study, we determined the near-atomic resolution cryo-EM structure of infectious, ex vivo mouse prion fibrils from the ME7 prion strain and compared this with the RML fibril structure. This structural comparison of two biologically distinct mouse-adapted prion strains suggests defined folding subdomains of PrP rungs and the way in which they are interrelated, providing a structural definition of intra-species prion strain-specific conformations. #1: ジャーナル: Biorxiv / 年: 2023 タイトル: A structural basis for prion strain diversity 著者: Manka, S.W. / Wenborn, A. / Betts, J. / Joiner, S. / Saibil, H.R. / Collinge, J. / Wadsworth, J.D.F. | ||||||||||||||||||
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 | 8a00.cif.gz | 77 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8a00.ent.gz | 61.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8a00.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a0/8a00 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/8a00 | HTTPS FTP |
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-関連構造データ
関連構造データ | 15043MC 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 15776.630 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P04925 |
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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 |
-試料調製
構成要素 | 名称: amyloid fibril of prion protein / タイプ: COMPLEX / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
緩衝液 | pH: 6.8 |
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 |
-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: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 49 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: -0.54 ° / 軸方向距離/サブユニット: 4.8 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 40239 / 対称性のタイプ: HELICAL | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL |