+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-40220 | |||||||||
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タイトル | 96-nm repeat unit of doublet microtubules from Chlamydomonas reinhardtii flagella | |||||||||
マップデータ | composite map of the 96 nm repeat from C. reinhardtii | |||||||||
試料 |
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キーワード | cilia (繊毛) / microtubule (微小管) / dynein (ダイニン) / MOTOR PROTEIN (モータータンパク質) | |||||||||
機能・相同性 | 機能・相同性情報 axonemal central pair / inner dynein arm / axonemal outer doublet / radial spoke head / outer dynein arm / axonemal dynein complex / axonemal dynein complex assembly / radial spoke / intraciliary transport particle B / outer dynein arm assembly ...axonemal central pair / inner dynein arm / axonemal outer doublet / radial spoke head / outer dynein arm / axonemal dynein complex / axonemal dynein complex assembly / radial spoke / intraciliary transport particle B / outer dynein arm assembly / inner dynein arm assembly / cilium-dependent cell motility / positive regulation of cilium-dependent cell motility / cellular anatomical entity / membrane-bounded organelle / regulation of cilium beat frequency involved in ciliary motility / dynein light chain binding / kinocilium / intraciliary transport / cilium movement involved in cell motility / establishment of protein localization to organelle / 9+2 motile cilium / cilium movement / dynein heavy chain binding / axoneme assembly / motile cilium assembly / cilium organization / axonemal microtubule / intracellular organelle / blue light photoreceptor activity / cell projection organization / negative regulation of microtubule depolymerization / dynein complex / nucleoside-diphosphate kinase / misfolded protein binding / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / myosin II complex / dynein light intermediate chain binding / Set1C/COMPASS complex / UTP biosynthetic process / ciliary plasm / CTP biosynthetic process / 酸化還元酵素 / 繊毛 / GTP biosynthetic process / microtubule associated complex / nucleoside diphosphate kinase activity / microtubule motor activity / ciliary base / dynein intermediate chain binding / dynein complex binding / beta-tubulin binding / microtubule-based movement / axoneme / chaperone cofactor-dependent protein refolding / mitotic cytokinesis / alpha-tubulin binding / cilium assembly / cellular response to unfolded protein / enzyme regulator activity / microtubule-based process / protein peptidyl-prolyl isomerization / regulation of microtubule cytoskeleton organization / protein folding chaperone / Hsp70 protein binding / heat shock protein binding / 中心小体 / FAD binding / 葉緑体 / GTPase activator activity / mitotic spindle organization / acrosomal vesicle / ciliary basal body / プロリルイソメラーゼ / peptidyl-prolyl cis-trans isomerase activity / cell projection / 運動性 / 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 / 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 / Hsp90 protein binding / 繊毛 / structural constituent of cytoskeleton / 紡錘体 / small GTPase binding / unfolded protein binding / フォールディング / mitotic cell cycle / protein-folding chaperone binding / protein refolding / microtubule binding / 微小管 / oxidoreductase activity / 細胞骨格 / calmodulin binding / hydrolase activity / 細胞周期 / 細胞分裂 / リン酸化 / GTPase activity 類似検索 - 分子機能 | |||||||||
生物種 | Chlamydomonas reinhardtii (クラミドモナス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | |||||||||
データ登録者 | Walton T / Brown A | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Nature / 年: 2023 タイトル: Axonemal structures reveal mechanoregulatory and disease mechanisms. 著者: Travis Walton / Miao Gui / Simona Velkova / Mahmoud R Fassad / Robert A Hirst / Eric Haarman / Christopher O'Callaghan / Mathieu Bottier / Thomas Burgoyne / Hannah M Mitchison / Alan Brown / 要旨: Motile cilia and flagella beat rhythmically on the surface of cells to power the flow of fluid and to enable spermatozoa and unicellular eukaryotes to swim. In humans, defective ciliary motility can ...Motile cilia and flagella beat rhythmically on the surface of cells to power the flow of fluid and to enable spermatozoa and unicellular eukaryotes to swim. In humans, defective ciliary motility can lead to male infertility and a congenital disorder called primary ciliary dyskinesia (PCD), in which impaired clearance of mucus by the cilia causes chronic respiratory infections. Ciliary movement is generated by the axoneme, a molecular machine consisting of microtubules, ATP-powered dynein motors and regulatory complexes. The size and complexity of the axoneme has so far prevented the development of an atomic model, hindering efforts to understand how it functions. Here we capitalize on recent developments in artificial intelligence-enabled structure prediction and cryo-electron microscopy (cryo-EM) to determine the structure of the 96-nm modular repeats of axonemes from the flagella of the alga Chlamydomonas reinhardtii and human respiratory cilia. Our atomic models provide insights into the conservation and specialization of axonemes, the interconnectivity between dyneins and their regulators, and the mechanisms that maintain axonemal periodicity. Correlated conformational changes in mechanoregulatory complexes with their associated axonemal dynein motors provide a mechanism for the long-hypothesized mechanotransduction pathway to regulate ciliary motility. Structures of respiratory-cilia doublet microtubules from four individuals with PCD reveal how the loss of individual docking factors can selectively eradicate periodically repeating structures. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
-関連構造データ
-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_40220.map.gz / 形式: CCP4 / 大きさ: 1.3 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | composite map of the 96 nm repeat from C. reinhardtii | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.36 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
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+追加マップ: position 1 of DMT - focused refinement 3 - postprocess
+追加マップ: position 4 of DMT - focused refinement 4 - postprocess
+追加マップ: position 4 of DMT - focused refinement 4 - mask
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+追加マップ: position 4 of DMT - focused refinement 4 - half map 1
+追加マップ: position 4 of DMT - focused refinement 1 - mask
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+追加マップ: position 4 of DMT - focused refinement 1 - postprocess
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+追加マップ: position 4 of DMT - focused refinement 2 - half map 2
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-試料の構成要素
+全体 : 96-nm repeat unit of doublet microtubules from the flagella of Ch...
+超分子 #1: 96-nm repeat unit of doublet microtubules from the flagella of Ch...
+分子 #1: Tubulin beta
+分子 #2: Tubulin alpha
+分子 #3: PACRG
+分子 #4: Cilia- and flagella-associated protein 20
+分子 #5: Meiosis-specific nuclear structural protein 1
+分子 #6: Flagellar associated protein
+分子 #7: Coiled-coil protein associated with protofilament ribbons
+分子 #8: Cilia- and flagella-associated protein 45
+分子 #9: FAP34
+分子 #10: Flagellar associated protein
+分子 #11: Protein Flattop homolog
+分子 #12: FAP52
+分子 #13: Nucleoside diphosphate kinase
+分子 #14: Flagellar associated protein
+分子 #15: Flagellar associated protein
+分子 #16: Flagellar associated protein
+分子 #17: FAP143
+分子 #18: Flagellar associated protein
+分子 #19: FAP166
+分子 #20: Flagellar associated protein
+分子 #21: FAP339
+分子 #22: Protofilament ribbon protein of flagellar microtubules
+分子 #23: Flagellar associated protein
+分子 #24: Flagellar associated protein
+分子 #25: Flagellar associated protein
+分子 #26: Flagellar associated protein
+分子 #27: FAP129
+分子 #28: FAP21
+分子 #29: Flagellar associated protein
+分子 #30: Flagellar associated protein
+分子 #31: FAP306
+分子 #32: Flagellar associated protein
+分子 #33: Flagellar associated protein
+分子 #34: Dynein axonemal light chain 1
+分子 #35: Outer dynein arm-docking complex subunit 1
+分子 #36: Outer dynein arm-docking complex protein DC3
+分子 #37: Dynein gamma chain, flagellar outer arm
+分子 #38: IC97/Casc1 N-terminal domain-containing protein
+分子 #39: Axonemal inner arm I1 intermediate chain dynein IC138
+分子 #40: IC140
+分子 #41: Axonemal inner arm dynein I1/f subunit
+分子 #42: Dynein light chain roadblock LC7b
+分子 #43: Dynein light chain roadblock LC7a
+分子 #44: Dynein 8 kDa light chain, flagellar outer arm
+分子 #45: Dynein light chain Tctex1
+分子 #46: Inner arm dynein light chain
+分子 #47: Dynein light chain 10
+分子 #48: Cilia- and flagella-associated protein 73
+分子 #49: Cilia- and flagella-associated protein 100
+分子 #50: Dynein, 78 kDa intermediate chain, flagellar outer arm
+分子 #51: WD_REPEATS_REGION domain-containing protein
+分子 #52: Flagellar outer dynein arm light chain 2
+分子 #53: Dynein 18 kDa light chain, flagellar outer arm
+分子 #54: Dynein 11 kDa light chain, flagellar outer arm
+分子 #55: Dynein light chain 9
+分子 #56: Outer dynein arm protein 1
+分子 #57: AAA+ ATPase domain-containing protein
+分子 #58: Dynein-1-beta heavy chain, flagellar inner arm I1 complex
+分子 #59: WD_REPEATS_REGION domain-containing protein
+分子 #60: Inner-arm dynein f/I1 light chain
+分子 #61: Heavy chain alpha
+分子 #62: Flagellar outer dynein arm heavy chain beta
+分子 #63: Dynein 14 kDa light chain, flagellar outer arm
+分子 #64: Dynein 16 kDa light chain, flagellar outer arm
+分子 #65: FAP44
+分子 #66: FAP43
+分子 #67: Dynein regulatory complex protein 1
+分子 #68: Dynein regulatory complex subunit 2
+分子 #69: Dynein regulatory complex subunit 6
+分子 #70: Dynein regulatory complex subunit 4
+分子 #71: Dynein regulatory complex protein 8
+分子 #72: ATPase AAA-type core domain-containing protein
+分子 #73: Flagellar associated protein
+分子 #74: Dynein regulatory complex subunit 3
+分子 #75: Dynein regulatory complex protein 9
+分子 #76: Dynein regulatory complex protein 10
+分子 #77: DRC5
+分子 #78: DUF4201 domain-containing protein
+分子 #79: Calmodulin
+分子 #80: Caltractin
+分子 #81: AAA+ ATPase domain-containing protein
+分子 #82: DUF4201 domain-containing protein
+分子 #83: Cilia- and flagella-associated protein 299
+分子 #84: Cilia- and flagella-associated protein 53
+分子 #85: FAP210
+分子 #86: Actin
+分子 #87: Flagellar radial spoke protein 5
+分子 #88: Flagellar radial spoke protein 1
+分子 #89: Flagellar radial spoke protein 2
+分子 #90: Radial spoke protein 3
+分子 #91: Radial spoke protein 4
+分子 #92: Flagellar radial spoke protein 6
+分子 #93: Radial spoke protein 7
+分子 #94: Radial spoke protein 9
+分子 #95: Radial spoke protein 10
+分子 #96: Radial spoke protein 11
+分子 #97: Peptidyl-prolyl cis-trans isomerase
+分子 #98: Radial spoke protein 14
+分子 #99: Radial spoke protein 16
+分子 #100: UNKNOWN
+分子 #101: Nucleoside diphosphate kinase 6
+分子 #102: Cytochrome b5 heme-binding domain-containing protein
+分子 #103: FAP385
+分子 #104: FAP207
+分子 #105: FAP253
+分子 #106: 28 kDa inner dynein arm light chain, axonemal
+分子 #107: AAA+ ATPase domain-containing protein
+分子 #108: UNKNOWN
+分子 #109: Radial spoke protein 15
+分子 #110: Radial spike protein 8
+分子 #111: DHC_N2 domain-containing protein
+分子 #112: Flagellar-associated protein 59
+分子 #113: Flagellar-associated protein 172
+分子 #114: Flagellar associated protein
+分子 #115: Cilia- and flagella-associated protein 58
+分子 #116: FAP251
+分子 #117: Cilia- and flagella-associated protein 61
+分子 #118: DHC2
+分子 #119: Subunit of axonemal inner dynein
+分子 #120: Subunit of axonemal inner dynein
+分子 #121: CFAP91 domain-containing protein
+分子 #122: AAA+ ATPase domain-containing protein
+分子 #123: AAA+ ATPase domain-containing protein
+分子 #124: Cilia- and flagella-associated protein 77
+分子 #125: Flagellar associated protein
+分子 #126: Flagellar associated protein
+分子 #127: FAP1
+分子 #128: GUANOSINE-5'-TRIPHOSPHATE
+分子 #129: GUANOSINE-5'-DIPHOSPHATE
+分子 #130: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | filament |
-試料調製
濃度 | 20 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
緩衝液 | pH: 7.4 構成要素:
| |||||||||||||||
グリッド | モデル: C-flat-1.2/1.3 / 材質: COPPER / 前処理 - タイプ: GLOW DISCHARGE | |||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 298 K / 装置: FEI VITROBOT MARK IV 詳細: 2.5 microliters of splayed axoneme sample at 16-26 mg/mL were applied to glow-discharged C-Flat 1.2/1.3-4Cu grids at 100% humidity. The samples were then incubated 10 s, blotted for 10 s, and ...詳細: 2.5 microliters of splayed axoneme sample at 16-26 mg/mL were applied to glow-discharged C-Flat 1.2/1.3-4Cu grids at 100% humidity. The samples were then incubated 10 s, blotted for 10 s, and plunged into liquid ethane. | |||||||||||||||
詳細 | Axonemes were splayed using 10 mM ATP and 0.75 mM CaCl2 for one hour at room temperature before centrifugation and resuspension. |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
---|---|
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 FIELDBright-field microscopy / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.5 µm / 倍率(公称値): 64000 |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 実像数: 36918 / 平均露光時間: 3.7 sec. / 平均電子線量: 61.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 8546747 詳細: Particles were manually picked as start/end coordinates. |
---|---|
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1.1) |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3.1.1) |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 詳細: Map resolution varies from 3.1 to 16.7 A. / 使用した粒子像数: 261585 |