+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4168 | |||||||||
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タイトル | Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1 | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Cryo-EM / Complex / MOTOR PROTEIN / dynein/dynactin/BICDR / TDR | |||||||||
機能・相同性 | 機能・相同性情報 RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Clathrin-mediated endocytosis / RHOF GTPase cycle / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / transport along microtubule / visual behavior / WASH complex / F-actin capping protein complex / positive regulation of intracellular transport / dynein light chain binding / negative regulation of filopodium assembly / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / axonemal dynein complex / positive regulation of spindle assembly / ciliary tip / structural constituent of postsynaptic actin cytoskeleton / vesicle transport along microtubule / dense body / Intraflagellar transport / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / P-body assembly / minus-end-directed microtubule motor activity / barbed-end actin filament capping / dynein light intermediate chain binding / cytoplasmic dynein complex / regulation of cell morphogenesis / retrograde axonal transport / RHO GTPases activate IQGAPs / regulation of lamellipodium assembly / RHO GTPases Activate Formins / nuclear migration / 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 / centrosome localization / microtubule motor activity / dynein intermediate chain binding / dynein complex binding / NuA4 histone acetyltransferase complex / microtubule-based movement / cytoplasmic microtubule / dynactin binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / Mitotic Prometaphase / cytoplasmic microtubule organization / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / axon cytoplasm / Recruitment of mitotic centrosome proteins and complexes / cytoskeleton organization / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / axonogenesis / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cell motility / actin filament / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / cell morphogenesis / kinetochore / small GTPase binding / cilium / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events 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 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
データ登録者 | Urnavicius L / Lau CK | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Nature / 年: 2018 タイトル: Cryo-EM shows how dynactin recruits two dyneins for faster movement. 著者: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter / 要旨: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_4168.map.gz | 31.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4168-v30.xml emd-4168.xml | 53.8 KB 53.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4168.png | 141.9 KB | ||
Filedesc metadata | emd-4168.cif.gz | 10.2 KB | ||
その他 | emd_4168_additional_1.map.gz emd_4168_additional_2.map.gz | 290.3 MB 770.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4168 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4168 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4168_validation.pdf.gz | 204.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4168_full_validation.pdf.gz | 203.9 KB | 表示 | |
XML形式データ | emd_4168_validation.xml.gz | 8.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4168 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4168 | HTTPS FTP |
-関連構造データ
関連構造データ | 6f1tMC 4169C 4170C 4171C 4172C 4177C 5owoC 6f1uC 6f1vC 6f1yC 6f1zC 6f38C 6f3aC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_4168.map.gz / 形式: CCP4 / 大きさ: 824 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: #1
ファイル | emd_4168_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #2
ファイル | emd_4168_additional_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Cryo-EM map of two dynein tail domains bound to dynactin and BICDR1
+超分子 #1: Cryo-EM map of two dynein tail domains bound to dynactin and BICDR1
+超分子 #2: BICD family-like cargo adapter 1
+超分子 #3: Dynein
+超分子 #4: Dynactin
+分子 #1: ARP1 actin related protein 1 homolog A
+分子 #2: Actin, cytoplasmic 1
+分子 #3: Actin related protein 10 homolog
+分子 #4: Capping protein (Actin filament) muscle Z-line, alpha 1
+分子 #5: F-actin capping protein beta subunit
+分子 #6: Dynactin Subunit 2
+分子 #7: Dynactin Subunit 2
+分子 #8: Dynactin Subunit 3
+分子 #9: Dynactin Subunit 2
+分子 #10: Dynactin 6
+分子 #11: Dynactin subunit 5
+分子 #12: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1...
+分子 #13: Dynactin Subunit 4
+分子 #14: Dynactin Subunit 1
+分子 #15: Dynactin subunit 2
+分子 #16: Dynactin subunit 2
+分子 #17: Dynactin subunit 2
+分子 #18: Dynactin subunit 2
+分子 #19: Cytoplasmic dynein 1 heavy chain 1,Cytoplasmic dynein 1 heavy cha...
+分子 #20: Cytoplasmic dynein 1 intermediate chain 2
+分子 #21: Cytoplasmic dynein 1 light intermediate chain 2
+分子 #22: Dynein light chain roadblock-type 1
+分子 #23: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1...
+分子 #24: Dynactin Subunit 1
+分子 #25: ADENOSINE-5'-DIPHOSPHATE
+分子 #26: ADENOSINE-5'-TRIPHOSPHATE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.4 |
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凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK III |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 52.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: EMDB MAP EMDB ID: 詳細: Initial model low pass filtered to 50 A |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 205611 |
初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION |
-原子モデル構築 1
詳細 | Refinement of Dynein chains (chains f, h, j, m, o, s, t) performed using related maps. Coordinates from these chains were used for the other dynein chains, refining into 5 and 8 A maps, then removing sidechains. Dynactin and parts of dyneins refined into this 3.5 A map. |
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精密化 | 空間: REAL 当てはまり具合の基準: Cross-correlation coefficient |
得られたモデル | PDB-6f1t: |