+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6rza | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of the human inner arm dynein DNAH7 microtubule binding domain bound to microtubules | |||||||||
要素 |
| |||||||||
キーワード | MOTOR PROTEIN / filament / complex | |||||||||
機能・相同性 | 機能・相同性情報 inner dynein arm / inner dynein arm assembly / axonemal dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cilium movement involved in cell motility / 9+2 motile cilium / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport ...inner dynein arm / inner dynein arm assembly / axonemal dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cilium movement involved in cell motility / 9+2 motile cilium / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium movement / regulation of metaphase plate congression / Resolution of Sister Chromatid Cohesion / establishment of spindle localization / positive regulation of spindle assembly / RHO GTPases Activate Formins / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / manchette / dynein complex / MHC class II antigen presentation / minus-end-directed microtubule motor activity / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / 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 / nuclear migration / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule motor activity / dynein intermediate chain binding / cytoplasmic microtubule / cytoplasmic microtubule organization / stress granule assembly / regulation of mitotic spindle organization / axon cytoplasm / Neutrophil degranulation / mitotic spindle organization / filopodium / 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 / cilium / structural constituent of cytoskeleton / microtubule cytoskeleton organization / nuclear envelope / microtubule cytoskeleton / mitotic cell cycle / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / axon / GTPase activity / centrosome / neuronal cell body / calcium ion binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) Homo sapiens (ヒト) Sus scrofa (ブタ) | |||||||||
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: 4.5 Å | |||||||||
データ登録者 | Lacey, S.E. / He, S. / Scheres, S.H.W. / Carter, A.P. | |||||||||
資金援助 | 英国, 2件
| |||||||||
引用 | ジャーナル: Elife / 年: 2019 タイトル: Cryo-EM of dynein microtubule-binding domains shows how an axonemal dynein distorts the microtubule. 著者: Samuel E Lacey / Shaoda He / Sjors Hw Scheres / Andrew P Carter / 要旨: Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain ...Dyneins are motor proteins responsible for transport in the cytoplasm and the beating of axonemes in cilia and flagella. They bind and release microtubules via a compact microtubule-binding domain (MTBD) at the end of a coiled-coil stalk. We address how cytoplasmic and axonemal dynein MTBDs bind microtubules at near atomic resolution. We decorated microtubules with MTBDs of cytoplasmic dynein-1 and axonemal dynein DNAH7 and determined their cryo-EM structures using helical Relion. The majority of the MTBD is rigid upon binding, with the transition to the high-affinity state controlled by the movement of a single helix at the MTBD interface. DNAH7 contains an 18-residue insertion, found in many axonemal dyneins, that contacts the adjacent protofilament. Unexpectedly, we observe that DNAH7, but not dynein-1, induces large distortions in the microtubule cross-sectional curvature. This raises the possibility that dynein coordination in axonemes is mediated via conformational changes in the microtubule. | |||||||||
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 | 6rza.cif.gz | 389.9 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6rza.ent.gz | 312 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6rza.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 | 6rza_validation.pdf.gz | 1.8 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6rza_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 6rza_validation.xml.gz | 68.1 KB | 表示 | |
CIF形式データ | 6rza_validation.cif.gz | 98.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rza ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rza | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCSアンサンブル:
|
-要素
-タンパク質 , 3種, 5分子 XACBD
#1: タンパク質 | 分子量: 18133.164 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from ...詳細: Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end,Fusion between two proteins. Cytoplasmic dynein 1 sequence from position 1 to 15 DNAH7 sequence from proline at position 16 to proline at position 154 Cytoplasmic dynein 1 sequence again from from 155 to end 由来: (組換発現) Mus musculus (ハツカネズミ), (組換発現) Homo sapiens (ヒト) 遺伝子: Dync1h1, Dhc1, Dnch1, Dnchc1, Dyhc, DNAH7, KIAA0944 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9JHU4, UniProt: Q8WXX0 | ||
---|---|---|---|
#2: タンパク質 | 分子量: 48679.051 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 器官: Brain / 参照: UniProt: Q2XVP4 #3: タンパク質 | 分子量: 47825.859 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 器官: Brain / 参照: UniProt: P02554 |
-非ポリマー , 4種, 8分子
#4: 化合物 | #5: 化合物 | #6: 化合物 | #7: 化合物 | |
---|
-詳細
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: HELICAL ARRAY / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
由来(天然) |
| ||||||||||||||||||||||||
由来(組換発現) | 生物種: Escherichia coli (大腸菌) | ||||||||||||||||||||||||
緩衝液 | pH: 8 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
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: 67.5 e/Å2 / 検出モード: INTEGRATING 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: REFMAC / バージョン: 5.8.0247 / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EMソフトウェア |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 41984 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | 解像度: 4.5→4.5 Å / Cor.coef. Fo:Fc: 0.582 / SU B: 243.237 / SU ML: 2.563 / ESU R: 2.187 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 206.247 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: 1 / 解像度: 5.402→195.3 Å / 合計: 14908 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|