+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j8x | ||||||
---|---|---|---|---|---|---|---|
タイトル | High-resolution structure of no-nucleotide kinesin on microtubules | ||||||
要素 |
| ||||||
キーワード | MOTOR PROTEIN/STRUCTURAL PROTEIN / molecular motors / kinesin / myosin / microtubules / cytoskeletal motors / MOTOR PROTEIN-STRUCTURAL PROTEIN complex | ||||||
機能・相同性 | 機能・相同性情報 plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / stress granule disassembly / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / mitochondrion transport along microtubule / centrosome localization / ciliary rootlet / microtubule motor activity / natural killer cell mediated cytotoxicity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / microtubule-based process / centriolar satellite / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / mitotic cell cycle / microtubule binding / vesicle / microtubule / cadherin binding / GTPase activity / GTP binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Sus scrofa (ブタ) | ||||||
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: 5 Å | ||||||
データ登録者 | Shang, Z. / Zhou, K. / Xu, C. / Csencsits, R. / Cochran, J.C. / Sindelar, C.V. | ||||||
引用 | ジャーナル: Elife / 年: 2014 タイトル: High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force-generation. 著者: Zhiguo Shang / Kaifeng Zhou / Chen Xu / Roseann Csencsits / Jared C Cochran / Charles V Sindelar / 要旨: Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing ...Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing atomic models for no-nucleotide and ATP states of the monomeric kinesin motor domain on microtubules from cryo-EM reconstructions at 5-6 Å resolution. By comparing these models with existing X-ray structures of ADP-bound kinesin, we infer a mechanistic scheme in which microtubule attachment, mediated by a universally conserved 'linchpin' residue in kinesin (N255), triggers a clamshell opening of the nucleotide cleft and accompanying release of ADP. Binding of ATP re-closes the cleft in a manner that tightly couples to translocation of cargo, via kinesin's 'neck linker' element. These structural transitions are reminiscent of the analogous nucleotide-exchange steps in the myosin and F1-ATPase motors and inform how the two heads of a kinesin dimer 'gate' each other to promote coordinated stepping along microtubules. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3j8x.cif.gz | 221.7 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb3j8x.ent.gz | 166.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j8x.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 | 3j8x_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 3j8x_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 3j8x_validation.xml.gz | 40.3 KB | 表示 | |
CIF形式データ | 3j8x_validation.cif.gz | 59.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8x ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8x | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
対称性 | らせん対称: (回転対称性: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 1 / Rise per n subunits: 8.78 Å / Rotation per n subunits: -25.77 °) |
詳細 | The reconstructed 14-protofilament microtubule is pseudo-symmetric, containing a seam with 3 starts per tubulin monomer, or 1.5 starts per tubulin dimer. |
-要素
#1: タンパク質 | 分子量: 39238.145 Da / 分子数: 1 断片: Truncated catalytic head domain (monomeric, UNP residues 1-349) 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KIF5B, KNS, KNS1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P33176 |
---|---|
#2: タンパク質 | 分子量: 50204.445 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: Q2XVP4 |
#3: タンパク質 | 分子量: 49983.824 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: F2Z5B2 |
#4: 化合物 | ChemComp-GTP / |
#5: 化合物 | ChemComp-GDP / |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 値: 0.135 MDa / 実験値: NO | |||||||||||||||||||||||||
緩衝液 | 名称: 25 mM PIPES, 25 mM NaCl, 2 mM MgCl2, 1 mM EGTA / pH: 6.8 / 詳細: 25 mM PIPES, 25 mM NaCl, 2 mM MgCl2, 1 mM EGTA | |||||||||||||||||||||||||
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: 300 mesh copper grid with homemade holey carbon | |||||||||||||||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 詳細: No glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequently, blotting and plunge freezing were ...詳細: No glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequently, blotting and plunge freezing were performed with ~0.5 second delay after blotting but prior to plunging into liquid ethane. 手法: No glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequently, blotting and plunge freezing were ...手法: No glow discharge was applied. After sample application to grid, liquid was mostly 'wicked' away by edgewise application of filter paper. Subsequently, blotting and plunge freezing were performed with ~0.5 second delay after blotting but prior to plunging. |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai F30 / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TECNAI F30 / 日付: 2013年4月15日 詳細: 8K x 8K super-resolution mode was used. 10 frames total were collected. |
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 FIELD / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2 mm / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN |
撮影 | 電子線照射量: 15 e/Å2 / フィルム・検出器のモデル: GATAN K2 (4k x 4k) |
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 | 相対比: 1 |
-解析
EMソフトウェア |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: done within FREALIGN | ||||||||||||
らせん対称 | 回転角度/サブユニット: 25.77 ° / 軸方向距離/サブユニット: 8.78 Å / らせん対称軸の対称性: C1 詳細: The reconstructed 14-protofilament microtubule is pseudo-symmetric, containing a seam with 3 starts per tubulin monomer, or 1.5 starts per tubulin dimer. | ||||||||||||
3次元再構成 | 手法: Single particle / 解像度: 5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 120783 / ピクセルサイズ(公称値): 1.99 Å / ピクセルサイズ(実測値): 1.99 Å 詳細: Initial alignment was done using customized SPIDER scripts. Reconstruction and subsequent refinement were done by FREALIGN. 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 Target criteria: RMSD from the starting structure was monitored for convergence. 詳細: REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation. Side chains were excluded from the MDFF target potential. Following several equilibration steps, the ...詳細: REFINEMENT PROTOCOL--flexible DETAILS--MDFF was performed using explicit solvation. Side chains were excluded from the MDFF target potential. Following several equilibration steps, the relative strength of the EM map potential (GSCALE term) was slowly increased from 0 to 1 over the course of 10 nanoseconds. The t = 1.2 ns time point was selected to represent the final fitted model, based on the approximate convergence of the RMSD from the starting structure. | ||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Accession code: 4HNA / Initial refinement model-ID: 1 / PDB-ID: 4HNA / Source name: PDB / タイプ: experimental model
| ||||||||||||
精密化ステップ | サイクル: LAST
|