+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-24664 | |||||||||
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タイトル | Composite cryo-EM density map of the 48-nm repeat doublet microtubule from bovine tracheal cilia | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | cilia / microtubule / dynein / motility / STRUCTURAL PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 regulation of cilium beat frequency / mucociliary clearance / outer dynein arm docking complex / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath ...regulation of cilium beat frequency / mucociliary clearance / outer dynein arm docking complex / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / protein polyglutamylation / sperm axoneme assembly / positive regulation of feeding behavior / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / cerebrospinal fluid circulation / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / outer dynein arm assembly / cilium-dependent cell motility / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / 9+2 motile cilium / 転移酵素; リンを含む基を移すもの / acrosomal membrane / MHC class II antigen presentation / ciliary transition zone / regulation of cilium assembly / cilium movement / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / Aggrephagy / axonemal microtubule / left/right axis specification / cilium organization / gamma-tubulin ring complex / The role of GTSE1 in G2/M progression after G2 checkpoint / flagellated sperm motility / 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 / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / ventricular system development / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / positive regulation of cilium assembly / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / microtubule organizing center / Neutrophil degranulation / intermediate filament / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary base / regulation of neuron projection development / beta-tubulin binding / axoneme / mitotic cytokinesis / centriolar satellite / spermatid development / cilium assembly / alpha-tubulin binding / cellular response to UV-C / sperm flagellum / single fertilization / sperm midpiece / Hsp70 protein binding / 3'-5' exonuclease activity / centriole / mitotic spindle organization / acrosomal vesicle / lung development / ciliary basal body / G protein-coupled receptor binding / 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 / Hsp90 protein binding / brain development / cilium / structural constituent of cytoskeleton / mitotic spindle / spindle pole 類似検索 - 分子機能 | |||||||||
生物種 | Bos taurus (ウシ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
データ登録者 | Gui M / Anderson JR / Botsch JJ / Meleppattu S / Singh SK / Zhang Q / Brown A | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Cell / 年: 2021 タイトル: De novo identification of mammalian ciliary motility proteins using cryo-EM. 著者: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James ...著者: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James Thompson / Jane S Lucas / Colin D Bingle / Dominic P Norris / Sudipto Roy / Alan Brown / 要旨: Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner ...Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility. | |||||||||
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
-検証レポート
文書・要旨 | emd_24664_validation.pdf.gz | 613.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_24664_full_validation.pdf.gz | 613.2 KB | 表示 | |
XML形式データ | emd_24664_validation.xml.gz | 19.6 KB | 表示 | |
CIF形式データ | emd_24664_validation.cif.gz | 27.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24664 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24664 | HTTPS FTP |
-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_24664.map.gz / 形式: CCP4 / 大きさ: 1.1 GB / 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: 1.09 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
+マスク #1
+追加マップ: consensus map
+追加マップ: local refined fragment 6-1
+追加マップ: local refined fragment 6-3
+追加マップ: local refined fragment 8-1
+追加マップ: local refined fragment 4-3
+追加マップ: local refined fragment 2-2
+追加マップ: local refined fragment 2-3
+追加マップ: local refined fragment 3-3
+追加マップ: local refined fragment 10-3
+追加マップ: local refined fragment 4-1
+追加マップ: deepemhancer postprocessing map
+追加マップ: local refined fragment of 8 tektin filaments 1
+追加マップ: local refined fragment 10-1
+追加マップ: local refined fragment 4-2
+追加マップ: local refined fragment 1-2
+追加マップ: local refined fragment of 8 tektin filaments 3
+追加マップ: local refined fragment 7-3
+追加マップ: local refined fragment 2-1
+追加マップ: local refined fragment 3-2
+追加マップ: local refined fragment 8-2
+追加マップ: local refined fragment 7-1
+追加マップ: local refined fragment 10-2
+追加マップ: local refined fragment 8-3
+追加マップ: local refined fragment 5-2
+追加マップ: local refined fragment 3-1
+追加マップ: local refined fragment 9-2
+追加マップ: local refined fragment 9-1
+追加マップ: local refined fragment of Pierce1/2 region 2
+追加マップ: multi-body local refined fragment of ODA-DC
+追加マップ: local refined fragment 1-3
+追加マップ: local refined fragment of Pierce1/2 region 1
+追加マップ: local refined fragment 9-3
+追加マップ: Overall cylinder mask
+追加マップ: local refined fragment of 8 tektin filaments 2
+追加マップ: local refined fragment 6-2
+追加マップ: local refined fragment 5-3
+追加マップ: local refined fragment 7-2
+追加マップ: local refined fragment 5-1
+追加マップ: local refined fragment 1-1
-試料の構成要素
+全体 : Doublet microtubule
+超分子 #1: Doublet microtubule
+分子 #1: Protein C9orf135 homolog
+分子 #2: EF-hand domain family member B
+分子 #3: Methyl-CpG binding domain protein 1
+分子 #4: Nucleoside diphosphate kinase 7
+分子 #5: Uncharacterized protein C1orf158 homolog
+分子 #6: Meiosis-specific nuclear structural protein 1
+分子 #7: Tektin-1
+分子 #8: Tubulin alpha-1D chain
+分子 #9: Tubulin beta-4B chain
+分子 #10: Tektin-2
+分子 #11: Uncharacterized protein C1orf189 homolog
+分子 #12: Tektin-3
+分子 #13: Sperm associated antigen 8
+分子 #14: Tektin-4
+分子 #15: Cilia and flagella associated protein 161
+分子 #16: TEKTIP1
+分子 #17: Pierce2
+分子 #18: Protein FAM166B
+分子 #19: Coiled-coil domain containing 114
+分子 #20: Outer dynein arm-docking complex subunit 3
+分子 #21: Armadillo repeat containing 4
+分子 #22: TTC25 protein
+分子 #23: EF-hand calcium-binding domain-containing protein 1
+分子 #24: RIB43A-like with coiled-coils protein 2
+分子 #25: EF-hand domain containing 1
+分子 #26: EFHC2
+分子 #27: Cilia- and flagella-associated protein 20
+分子 #28: PACRG protein
+分子 #29: Cilia and flagella associated protein 45
+分子 #30: Cilia and flagella associated protein 52
+分子 #31: Enkurin, TRPC channel interacting protein
+分子 #32: Protein Flattop
+分子 #33: Coiled-coil domain containing 173
+分子 #34: Chromosome 3 C1orf194 homolog
+分子 #35: EFCAB6
+分子 #36: Pierce1
+分子 #37: GUANOSINE-5'-TRIPHOSPHATE
+分子 #38: MAGNESIUM ION
+分子 #39: GUANOSINE-5'-DIPHOSPHATE
-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 | filament |
-試料調製
緩衝液 | pH: 7.4 |
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グリッド | 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-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: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 60.0 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | プロトコル: AB INITIO MODEL |
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得られたモデル | PDB-7rro: |