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基本情報
登録情報 | データベース: PDB / ID: 3zys | ||||||
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タイトル | Human dynamin 1 deltaPRD polymer stabilized with GMPPCP | ||||||
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![]() | HYDROLASE/GTP-BINDING PROTEIN / HYDROLASE-GTP-BINDING PROTEIN COMPLEX / ENDOCYTOSIS / GTP HYDROLYSIS / MEMBRANE REMODELING | ||||||
機能・相同性 | ![]() clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling ...clathrin coat assembly involved in endocytosis / vesicle scission / synaptic vesicle budding from presynaptic endocytic zone membrane / presynaptic endocytic zone membrane / interleukin-27-mediated signaling pathway / dynamin GTPase / chromaffin granule / regulation of vesicle size / Toll Like Receptor 4 (TLR4) Cascade / Retrograde neurotrophin signalling / Formation of annular gap junctions / endosome organization / Gap junction degradation / photoreceptor ribbon synapse / membrane coat / response to type I interferon / negative regulation of viral genome replication / Recycling pathway of L1 / phosphatidylinositol-3,4,5-trisphosphate binding / antiviral innate immune response / endocytic vesicle / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / MHC class II antigen presentation / photoreceptor inner segment / receptor-mediated endocytosis / cell projection / response to virus / modulation of chemical synaptic transmission / protein homooligomerization / receptor internalization / ISG15 antiviral mechanism / defense response / endocytosis / : / GDP binding / Interferon alpha/beta signaling / presynapse / Clathrin-mediated endocytosis / microtubule binding / nuclear membrane / protein homotetramerization / microtubule / defense response to virus / innate immune response / GTPase activity / glutamatergic synapse / apoptotic process / synapse / endoplasmic reticulum membrane / GTP binding / protein kinase binding / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / 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: 12.2 Å | ||||||
![]() | Chappie, J.S. / Mears, J.A. / Fang, S. / Leonard, M. / Schmid, S.L. / Milligan, R.A. / Hinshaw, J.E. / Dyda, F. | ||||||
![]() | ![]() タイトル: A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke. 著者: Joshua S Chappie / Jason A Mears / Shunming Fang / Marilyn Leonard / Sandra L Schmid / Ronald A Milligan / Jenny E Hinshaw / Fred Dyda / ![]() 要旨: The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process ...The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process remain a mystery. We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. The structures reveal the position and connectivity of dynamin fragments in the assembled structure, showing that G domain dimers only form between tetramers in sequential rungs of the dynamin helix. Using chemical crosslinking, we demonstrate that dynamin tetramers are made of two dimers, in which the G domain of one molecule interacts in trans with the GED of another. Structural comparison of GG(GMPPCP) to the GG transition-state complex identifies a hydrolysis-dependent powerstroke that may play a role in membrane-remodeling events necessary for fission. | ||||||
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 260.3 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 935.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1002 KB | 表示 | |
XML形式データ | ![]() | 47.9 KB | 表示 | |
CIF形式データ | ![]() | 70 KB | 表示 | |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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1 | ![]()
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3 | ![]()
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対称性 | らせん対称: (回転対称性: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 12 / Rise per n subunits: 15.045 Å / Rotation per n subunits: 54.545 °) |
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要素
#1: タンパク質 | 分子量: 39388.961 Da / 分子数: 2 断片: G DOMAIN, RESIDUES 1-320, GTPASE EFFECTOR DOMAIN, RESIDUES 726-750 由来タイプ: 組換発現 詳細: EIGHT AMINO ACID POLYPEPTIDE LINKER BETWEEN G DOMAIN AND GTPASE EFFECTOR DOMAIN, RESIDUES 321-328 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 75623.188 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #3: タンパク質 | 分子量: 13440.362 Da / 分子数: 2 / 断片: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 518-630 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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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: HELICAL ARRAY / 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: GMPPCP STABILIZED HUMAN DYNAMIN 1 DELTA PRD HELICAL POLYMER タイプ: COMPLEX 詳細: DELTA PRD DYNAMIN HELICAL TUBES GENERATED IN THE PRESENCE OF GMPPCP AND DOPS LIPOSOMES |
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緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 詳細: PLUNGE FROZEN IN LIQUID ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TECNAI F20 |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 10 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
放射波長 | 相対比: 1 |
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解析
EMソフトウェア |
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CTF補正 | 詳細: INDIVIDUAL IMAGES USING ACE2 | ||||||||||||||||||||||||||||
3次元再構成 | 手法: IHRSR / 解像度: 12.2 Å / 粒子像の数: 4814 / ピクセルサイズ(公称値): 2.26 Å 詳細: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS A AND D OF THE MODEL SHOW RESIDUES 6-311 OF HUMAN DYNAMIN 1'S G DOMAIN AND ...詳細: THIS MODEL INCORPORATES COORDINATES FROM 3ZYC AND 1DYN, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS A AND D OF THE MODEL SHOW RESIDUES 6-311 OF HUMAN DYNAMIN 1'S G DOMAIN AND RESIDUES 726-748 OF ITS GTPASE EFFECTOR DOMAIN. CHAINS C AND F INCLUDE RESIDUES 518-630 OF DYNAMIN'S PH DOMAIN. RESIDUE 5 SER IN CHAINS A AND D IS A CLONING ARTIFACT THAT WAS VISIBLE IN THE CRYSTAL STRUCTURE OF 3ZYC. INCORPORATES COORDINATES FROM 3LJB, WHICH WERE DOCKED INTO A HELICAL CRYO-EM DENSITY. CHAINS B AND E INCLUDE RESIDUES 367-435 AND 451-531 OF HUMAN MXA'S MIDDLE DOMAIN AND RESIDUES 576-636 OF IF GTPASE EFFECTOR DOMAIN. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1949. (DEPOSITION ID: 10194). 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 / 詳細: REFINEMENT PROTOCOL--YUP ALGORITHM | ||||||||||||||||||||||||||||
原子モデル構築 |
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精密化 | 最高解像度: 12.2 Å | ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 12.2 Å
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