+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6pen | ||||||
---|---|---|---|---|---|---|---|
タイトル | Structure of Spastin Hexamer (whole model) in complex with substrate peptide | ||||||
要素 |
| ||||||
キーワード | MOTOR PROTEIN / AAA+ ATPase / Microtubule Severing | ||||||
機能・相同性 | 機能・相同性情報 cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III ...cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane fission / microtubule bundle formation / anterograde axonal transport / mitotic spindle disassembly / protein hexamerization / exit from mitosis / axonal transport of mitochondrion / beta-tubulin binding / positive regulation of cytokinesis / mitotic cytokinesis / alpha-tubulin binding / endoplasmic reticulum to Golgi vesicle-mediated transport / axon cytoplasm / lipid droplet / axonogenesis / isomerase activity / protein homooligomerization / spindle pole / midbody / nuclear membrane / cytoplasmic vesicle / microtubule binding / microtubule / endosome / axon / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) synthetic construct (人工物) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.2 Å | ||||||
データ登録者 | Han, H. / Schubert, H.L. / McCullough, J. / Monroe, N. / Sundquist, W.I. / Hill, C.P. | ||||||
資金援助 | 米国, 1件
| ||||||
引用 | ジャーナル: J Biol Chem / 年: 2020 タイトル: Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. 著者: Han Han / Heidi L Schubert / John McCullough / Nicole Monroe / Michael D Purdy / Mark Yeager / Wesley I Sundquist / Christopher P Hill / 要旨: Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic ...Many members of the AAA+ ATPase family function as hexamers that unfold their protein substrates. These AAA unfoldases include spastin, which plays a critical role in the architecture of eukaryotic cells by driving the remodeling and severing of microtubules, which are cytoskeletal polymers of tubulin subunits. Here, we demonstrate that a human spastin binds weakly to unmodified peptides from the C-terminal segment of human tubulin α1A/B. A peptide comprising alternating glutamate and tyrosine residues binds more tightly, which is consistent with the known importance of glutamylation for spastin microtubule severing activity. A cryo-EM structure of the spastin-peptide complex at 4.2 Å resolution revealed an asymmetric hexamer in which five spastin subunits adopt a helical, spiral staircase configuration that binds the peptide within the central pore, whereas the sixth subunit of the hexamer is displaced from the peptide/substrate, as if transitioning from one end of the helix to the other. This configuration differs from a recently published structure of spastin from , which forms a six-subunit spiral without a transitioning subunit. Our structure resembles other recently reported AAA unfoldases, including the meiotic clade relative Vps4, and supports a model in which spastin utilizes a hand-over-hand mechanism of tubulin translocation and microtubule remodeling. | ||||||
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 | 6pen.cif.gz | 309.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6pen.ent.gz | 238.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6pen.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 | 6pen_validation.pdf.gz | 1 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6pen_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | 6pen_validation.xml.gz | 49.6 KB | 表示 | |
CIF形式データ | 6pen_validation.cif.gz | 73.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pe/6pen ftp://data.pdbj.org/pub/pdb/validation_reports/pe/6pen | HTTPS FTP |
-関連構造データ
関連構造データ | 20327MC 20805FC 6pekC |
---|---|
類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10382 (タイトル: Structure of spastin bound to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. Data size: 1.8 TB Data #1: Unaligned multi-frame movies of ADPBeFx-bound Spastin [micrographs - multiframe]) |
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
#1: タンパク質 | 分子量: 54498.328 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SPAST, ADPSP, FSP2, KIAA1083, SPG4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UBP0, microtubule-severing ATPase #2: タンパク質・ペプチド | | 分子量: 1479.453 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) #3: 化合物 | ChemComp-ADP / #4: 化合物 | ChemComp-BEF / #5: 化合物 | ChemComp-MG / 研究の焦点であるリガンドがあるか | N | |
---|
-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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Spastin Hexamer with a substrate peptide bound in the central pore タイプ: COMPLEX / Entity ID: #1-#2 / 由来: MULTIPLE SOURCES |
---|---|
分子量 | 実験値: NO |
緩衝液 | pH: 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 |
---|---|
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 FIELD |
撮影 | 電子線照射量: 57 e/Å2 フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.16_3549: / 分類: 精密化 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 119984 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
|