+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-41431 | ||||||||||||
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タイトル | 48-nm repeating structure of doublets from mouse sperm flagella | ||||||||||||
マップデータ | Final map of 48 nm-repeating unit of mouse sperm doublets | ||||||||||||
試料 |
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キーワード | Mammalian sperm / axoneme / microtubule-based structure / microtubule inner protein / non-motor proteins / cellular motility / fertility / structural protein | ||||||||||||
機能・相同性 | 機能・相同性情報 ERKs are inactivated / axonemal microtubule doublet inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / sperm flagellum assembly / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III ...ERKs are inactivated / axonemal microtubule doublet inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / left/right pattern formation / sperm flagellum assembly / establishment of left/right asymmetry / 9+0 motile cilium / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / outer acrosomal membrane / regulation of brood size / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath / regulation of calcineurin-NFAT signaling cascade / inner dynein arm assembly / Intraflagellar transport / axonemal A tubule inner sheath / Carboxyterminal post-translational modifications of tubulin / sperm axoneme assembly / protein polyglutamylation / MAP kinase phosphatase activity / positive regulation of feeding behavior / sperm principal piece / COPI-independent Golgi-to-ER retrograde traffic / cerebrospinal fluid circulation / cilium-dependent cell motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / regulation of cilium beat frequency involved in ciliary motility / regulation of store-operated calcium entry / protein tyrosine/serine/threonine phosphatase activity / COPI-mediated anterograde transport / Aggrephagy / intraciliary transport / 9+2 motile cilium / 転移酵素; リンを含む基を移すもの / Kinesins / acrosomal membrane / PKR-mediated signaling / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / ciliary transition zone / cilium movement / RHO GTPases activate IQGAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / calcium ion sensor activity / axoneme assembly / Recycling pathway of L1 / axonemal microtubule / left/right axis specification / cilium organization / COPI-dependent Golgi-to-ER retrograde traffic / flagellated sperm motility / RHO GTPases Activate Formins / gamma-tubulin ring complex / Separation of Sister Chromatids / Hedgehog 'off' state / organelle transport along microtubule / 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 / glial cell differentiation / AURKA Activation by TPX2 / forebrain morphogenesis / negative regulation of T cell activation / Regulation of PLK1 Activity at G2/M Transition / neuron projection arborization / manchette / cerebellar cortex morphogenesis / positive regulation of cilium assembly / dentate gyrus development / MHC class II antigen presentation / pyramidal neuron differentiation / negative regulation of JNK cascade / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / centrosome cycle / GTP biosynthetic process / microtubule organizing center / motor behavior / intermediate filament / response to L-glutamate / nucleoside diphosphate kinase activity / ciliary base / regulation of focal adhesion assembly / receptor clustering / negative regulation of T cell receptor signaling pathway / tubulin complex / smoothened signaling pathway / intercellular bridge / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity 類似検索 - 分子機能 | ||||||||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||||||||
手法 | サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 7.7 Å | ||||||||||||
データ登録者 | Chen Z / Shiozak M / Hass KM / Skinner W / Zhao S / Guo C / Polacco BJ / Yu Z / Krogan NJ / Kaake RM ...Chen Z / Shiozak M / Hass KM / Skinner W / Zhao S / Guo C / Polacco BJ / Yu Z / Krogan NJ / Kaake RM / Vale RD / Agard DA | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Cell / 年: 2023 タイトル: De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking. 著者: Zhen Chen / Momoko Shiozaki / Kelsey M Haas / Will M Skinner / Shumei Zhao / Caiying Guo / Benjamin J Polacco / Zhiheng Yu / Nevan J Krogan / Polina V Lishko / Robyn M Kaake / Ronald D Vale / David A Agard / 要旨: To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their ...To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their structures in vitro. Here, we combined cellular cryoelectron tomography (cryo-ET) and AlphaFold2 modeling to address these questions and understand how mammalian sperm are built in situ. Our cellular cryo-ET and subtomogram averaging provided 6.0-Å reconstructions of axonemal microtubule structures. The well-resolved tertiary structures allowed us to unbiasedly match sperm-specific densities with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105, and SPACA9 as novel microtubule-associated proteins. These proteins form an extensive interaction network crosslinking the lumen of axonemal doublet microtubules, suggesting their roles in modulating the mechanical properties of the filaments. Indeed, Tekt5 -/- sperm possess more deformed flagella with 180° bends. Together, our studies presented a cellular visual proteomics workflow and shed light on the in vivo functions of Tektin 5. | ||||||||||||
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
マップデータ | emd_41431.map.gz | 20.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-41431-v30.xml emd-41431.xml | 54.2 KB 54.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_41431.png | 136 KB | ||
Filedesc metadata | emd-41431.cif.gz | 16.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-41431 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41431 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_41431_validation.pdf.gz | 566.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_41431_full_validation.pdf.gz | 566.4 KB | 表示 | |
XML形式データ | emd_41431_validation.xml.gz | 6.3 KB | 表示 | |
CIF形式データ | emd_41431_validation.cif.gz | 7.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41431 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41431 | HTTPS FTP |
-関連構造データ
関連構造データ | 8to0MC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_41431.map.gz / 形式: CCP4 / 大きさ: 80.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Final map of 48 nm-repeating unit of mouse sperm doublets | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.65 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
-試料の構成要素
+全体 : Mouse sperm
+超分子 #1: Mouse sperm
+分子 #1: Cilia- and flagella-associated protein 95
+分子 #2: Tektin-1
+分子 #3: Detyrosinated tubulin alpha-1A chain
+分子 #4: Tubulin beta-4B chain
+分子 #5: Tektin-2
+分子 #6: EF-hand domain-containing family member B
+分子 #7: Tektin-3
+分子 #8: Meiosis-specific nuclear structural protein 1
+分子 #9: Tektin-4
+分子 #10: Cilia- and flagella-associated protein 53
+分子 #11: Tektin bundle-interacting protein 1
+分子 #12: Cilia- and flagella-associated protein 141
+分子 #13: Nucleoside diphosphate kinase 7
+分子 #14: Protein FAM166B
+分子 #15: Sperm-associated antigen 8
+分子 #16: RIB43A-like with coiled-coils protein 2
+分子 #17: Cilia- and flagella-associated protein 107
+分子 #18: Cilia- and flagella-associated protein 161
+分子 #19: EF-hand domain-containing protein 1
+分子 #20: Sperm acrosome-associated protein 9
+分子 #21: EF-hand domain-containing family member C2
+分子 #22: Cilia- and flagella-associated protein 20
+分子 #23: Parkin coregulated gene protein homolog
+分子 #24: Dual specificity protein phosphatase 3
+分子 #25: Piercer of microtubule wall 2 protein
+分子 #26: Tektin-5
+分子 #27: Cilia- and flagella-associated protein 45
+分子 #28: Cilia- and flagella-associated protein 52
+分子 #29: Enkurin
+分子 #30: Protein Flattop
+分子 #31: Cilia- and flagella- associated protein 210
+分子 #32: Cilia- and flagella-associated protein 276
+分子 #33: EF-hand calcium-binding domain-containing protein 6
+分子 #34: Coiled-coil domain-containing protein 105
+分子 #35: Piercer of microtubule wall 1 protein
-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 | サブトモグラム平均法 |
試料の集合状態 | cell |
-試料調製
緩衝液 | pH: 7.4 |
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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: 4.0 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 / 最大 デフォーカス(公称値): 6.0 µm / 最小 デフォーカス(公称値): 2.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
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: 7.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 4.0-beta2) / 使用したサブトモグラム数: 12848 |
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抽出 | トモグラム数: 76 / 使用した粒子像数: 32288 詳細: 32288 particles were initially picked every 24 nm along the microtubules. |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |