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基本情報
登録情報 | データベース: PDB / ID: 8rgh | ||||||||||||||||||||||||||||||
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タイトル | Structure of dynein-2 intermediate chain DYNC2I1 (WDR60) in complex with the dynein-2 heavy chain DYNC2H1. | ||||||||||||||||||||||||||||||
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![]() | TRANSPORT PROTEIN / dynein / cilia / intraflagellar transport / complex | ||||||||||||||||||||||||||||||
機能・相同性 | ![]() MGMT-mediated DNA damage reversal / intraciliary transport involved in cilium assembly / visual behavior / intraciliary retrograde transport / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / cilium movement involved in cell motility / 9+2 motile cilium / intraciliary transport / dynein light chain binding ...MGMT-mediated DNA damage reversal / intraciliary transport involved in cilium assembly / visual behavior / intraciliary retrograde transport / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / cilium movement involved in cell motility / 9+2 motile cilium / intraciliary transport / dynein light chain binding / ciliary transition zone / regulation of cilium assembly / spinal cord motor neuron differentiation / dynein heavy chain binding / DNA-methyltransferase activity / embryonic skeletal system morphogenesis / ciliary tip / Intraflagellar transport / dynein complex / DNA ligation / coronary vasculature development / minus-end-directed microtubule motor activity / non-motile cilium assembly / DNA alkylation repair / dynein light intermediate chain binding / protein localization to cilium / cytoplasmic dynein complex / positive regulation of smoothened signaling pathway / ciliary plasm / dorsal/ventral pattern formation / motile cilium / determination of left/right symmetry / embryonic limb morphogenesis / positive regulation of double-strand break repair / microtubule motor activity / ciliary base / dynein intermediate chain binding / pericentriolar material / microtubule-based movement / Golgi organization / cytoskeletal motor activity / axoneme / cilium assembly / Hedgehog 'off' state / forebrain development / centriole / ciliary basal body / filopodium / kidney development / methyltransferase activity / cilium / protein processing / apical part of cell / methylation / microtubule / DNA repair / centrosome / negative regulation of apoptotic process / Golgi apparatus / ATP hydrolysis activity / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||||||||||||||||||||
生物種 | ![]() | ||||||||||||||||||||||||||||||
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: 3.9 Å | ||||||||||||||||||||||||||||||
![]() | Mukhopadhyay, A.G. / Toropova, K. / Daly, L. / Wells, J. / Vuolo, L. / Seda, M. / Jenkins, D. / Stephens, D.J. / Roberts, A.J. | ||||||||||||||||||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. 著者: Aakash G Mukhopadhyay / Katerina Toropova / Lydia Daly / Jennifer N Wells / Laura Vuolo / Miroslav Mladenov / Marian Seda / Dagan Jenkins / David J Stephens / Anthony J Roberts / ![]() 要旨: Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. ...Dynein-2 is a large multiprotein complex that powers retrograde intraflagellar transport (IFT) of cargoes within cilia/flagella, but the molecular mechanism underlying this function is still emerging. Distinctively, dynein-2 contains two identical force-generating heavy chains that interact with two different intermediate chains (WDR34 and WDR60). Here, we dissect regulation of dynein-2 function by WDR34 and WDR60 using an integrative approach including cryo-electron microscopy and CRISPR/Cas9-enabled cell biology. A 3.9 Å resolution structure shows how WDR34 and WDR60 use surprisingly different interactions to engage equivalent sites of the two heavy chains. We show that cilia can assemble in the absence of either WDR34 or WDR60 individually, but not both subunits. Dynein-2-dependent distribution of cargoes depends more strongly on WDR60, because the unique N-terminal extension of WDR60 facilitates dynein-2 targeting to cilia. Strikingly, this N-terminal extension can be transplanted onto WDR34 and retain function, suggesting it acts as a flexible tether to the IFT "trains" that assemble at the ciliary base. We discuss how use of unstructured tethers represents an emerging theme in IFT train interactions. | ||||||||||||||||||||||||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 347.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 206.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.5 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.5 MB | 表示 | |
XML形式データ | ![]() | 51.4 KB | 表示 | |
CIF形式データ | ![]() | 78.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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要素
#1: タンパク質 | 分子量: 515223.031 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: DYNC2H1 with N-terminal SNAPf tag / 由来: (組換発現) ![]() 遺伝子: MGMT, DYNC2H1, DHC1B, DHC2, DNCH2, DYH1B, KIAA1997 発現宿主: ![]() ![]() 参照: UniProt: P16455, UniProt: Q8NCM8, methylated-DNA-[protein]-cysteine S-methyltransferase |
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#2: タンパク質 | 分子量: 122865.156 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q8WVS4 |
#3: タンパク質 | 分子量: 60639.129 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: DYNC2I2 (also known as WDR34) with C-terminal Strep tag 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q96EX3 |
#4: タンパク質 | 分子量: 39681.621 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q8TCX1 |
#5: タンパク質 | 分子量: 10934.576 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9NP97 |
-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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: Dynein-2 complex / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
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 |
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: FEI TITAN 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): 3500 nm / 最小 デフォーカス(公称値): 1500 nm |
撮影 | 電子線照射量: 50.6 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
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 113479 / 詳細: Global resolution 3.9A / 対称性のタイプ: POINT |