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基本情報
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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 | |||||||||
![]() | Cryo-EM map of protomer of the cytoplasmic ring of the Nuclear pore complex from Xenopus laevis. | |||||||||
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![]() | Nuclear pore complex / NUCLEAR PROTEIN | |||||||||
機能・相同性 | ![]() macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / macromolecule metabolic process / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore central transport channel ...macromolecule localization / nitrogen compound transport / GATOR2 complex / nephron development / macromolecule metabolic process / protein exit from endoplasmic reticulum / protein localization to nuclear inner membrane / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore organization / COPII vesicle coat / : / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / mRNA transport / cellular response to nutrient levels / mRNA export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / phospholipid binding / kinetochore / protein import into nucleus / protein transport / nuclear membrane / cell division / lysosomal membrane / positive regulation of DNA-templated transcription / structural molecule activity / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
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 | |||||||||
![]() | Fontana P / Wu H | |||||||||
資金援助 | 1件
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![]() | ![]() 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]. | |||||||||
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マップデータ | ![]() | 49.3 MB | ![]() | |
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文書・要旨 | ![]() | 479.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 479 KB | 表示 | |
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-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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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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
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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: ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | TFS 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: 1.25 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
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): 3.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: EMDB MAP EMDB ID: |
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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 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |