+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25817 | |||||||||
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タイトル | Cryo-EM map of protomer of the cytoplasmic ring of the nuclear pore complex from Xenopus laevis | |||||||||
マップデータ | Cryo-EM map of protomer of the cytoplasmic ring of the Nuclear pore complex from Xenopus laevis. | |||||||||
試料 |
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キーワード | Nuclear pore complex (核膜孔) / NUCLEAR PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / organic substance transport / macromolecule metabolic process / nuclear pore organization / nuclear pore outer ring / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore ...macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / organic substance transport / macromolecule metabolic process / nuclear pore organization / nuclear pore outer ring / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / nucleocytoplasmic transport / mitotic metaphase chromosome alignment / cellular response to nutrient levels / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / intracellular transport / mRNA transport / 核膜孔 / positive regulation of TORC1 signaling / 動原体 / protein transport / 核膜 / lysosomal membrane / 細胞分裂 / structural molecule activity / metal ion binding / 細胞核 / 細胞質基質 類似検索 - 分子機能 | |||||||||
生物種 | Xenopus laevis (アフリカツメガエル) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.9 Å | |||||||||
データ登録者 | Fontana P / Wu H | |||||||||
資金援助 | 1件
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引用 | ジャーナル: Science / 年: 2022 タイトル: Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold. 著者: Pietro Fontana / Ying Dong / Xiong Pi / Alexander B Tong / Corey W Hecksel / Longfei Wang / Tian-Min Fu / Carlos Bustamante / Hao Wu / 要旨: INTRODUCTION The nuclear pore complex (NPC) is the molecular conduit in the nuclear membrane of eukaryotic cells that regulates import and export of biomolecules between the nucleus and the cytosol, ...INTRODUCTION The nuclear pore complex (NPC) is the molecular conduit in the nuclear membrane of eukaryotic cells that regulates import and export of biomolecules between the nucleus and the cytosol, with vertebrate NPCs ~110 to 125 MDa in molecular mass and ~120 nm in diameter. NPCs are organized into four main rings: the cytoplasmic ring (CR) at the cytosolic side, the inner ring and the luminal ring on the plane of the nuclear membrane, and the nuclear ring facing the nucleus. Each ring possesses an approximate eightfold symmetry and is composed of multiple copies of different nucleoporins. NPCs have been implicated in numerous biological processes, and their dysfunctions are associated with a growing number of serious human diseases. However, despite pioneering studies from many groups over the past two decades, we still lack a full understanding of NPCs' organization, dynamics, and complexity. RATIONALE We used the oocyte as a model system for the structural characterization because each oocyte possesses a large number of NPC particles that can be visualized on native nuclear membranes without the aid of detergent extraction. We used single-particle cryo-electron microscopy (cryo-EM) analysis on data collected at different stage tilt angles for three-dimensional reconstruction and structure prediction with AlphaFold for model building. RESULTS We reconstructed the CR map of NPC at 6.9 and 6.7 Å resolutions for the full CR protomer and a core region, respectively, and predicted the structures of the individual nucleoporins using AlphaFold because no high-resolution models of Nups were available. For any ambiguous subunit interactions, we also predicted complex structures, which further guided model fitting of the CR protomer. We placed the nucleoporin or complex structures into the CR density to obtain an almost full CR atomic model, composed of the inner and outer Y-complexes, two copies of Nup205, two copies of the Nup214-Nup88-Nup62 complex, one Nup155, and five copies of Nup358. In particular, we predicted the largest protein in the NPC, Nup358, as having an S-shaped globular domain, a coiled-coil domain, and a largely disordered C-terminal region containing phenylalanine-glycine (FG) repeats previously shown to form a gel-like condensate phase for selective cargo passage. Four of the Nup358 copies clamp around the inner and outer Y-complexes to stabilize the CR, and the fifth Nup358 situates in the center of the cluster of clamps. AlphaFold also predicted a homo-oligomeric, likely specifically pentameric, coiled-coil structure of Nup358 that may provide the avidity for Nup358 recruitment to the NPC and for lowering the threshold for Nup358 condensation in NPC biogenesis. CONCLUSION Our studies offer an example of integrative cryo-EM and structure prediction as a general approach for attaining more precise models of megadalton protein complexes from medium-resolution density maps. The more accurate and almost complete model of the CR presented here expands our understanding of the molecular interactions in the NPC and represents a substantial step forward toward the molecular architecture of a full NPC, with implications for NPC function, biogenesis, and regulation. [Figure: see text]. | |||||||||
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_25817.map.gz | 49.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25817-v30.xml emd-25817.xml | 7.9 KB 7.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25817.png | 69.3 KB | ||
Filedesc metadata | emd-25817.cif.gz | 3.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25817 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25817 | HTTPS FTP |
-関連構造データ
関連構造データ | 7tdzMC 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 | 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_25817.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Cryo-EM map of protomer of the cytoplasmic ring of the Nuclear pore complex from Xenopus laevis. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.8 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 : Cytoplasmic ring of Nuclear Pore Complex
全体 | 名称: Cytoplasmic ring of Nuclear Pore Complex |
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要素 |
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-超分子 #1: Cytoplasmic ring of Nuclear Pore Complex
超分子 | 名称: Cytoplasmic ring of Nuclear Pore Complex / タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Xenopus laevis (アフリカツメガエル) |
-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: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
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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): 3.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
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: 1.25 e/Å2 |
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: |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 6.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 333214 |