+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12813 | |||||||||
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タイトル | Segment of the nucleoplasmic ring of the human nuclear pore complex | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / Seh1-associated complex / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction ...positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / Seh1-associated complex / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / telomere tethering at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore organization / nuclear pore complex assembly / nuclear pore outer ring / atrial cardiac muscle cell action potential / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / somite development / COPII vesicle coat / Nuclear Pore Complex (NPC) Disassembly / positive regulation of protein localization to centrosome / nuclear inclusion body / nuclear pore nuclear basket / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Amino acids regulate mTORC1 / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / positive regulation of mRNA splicing, via spliceosome / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Flemming body / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / negative regulation of programmed cell death / mitotic centrosome separation / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / neural tube development / COPII-mediated vesicle transport / poly(A)+ mRNA export from nucleus / lamellipodium assembly / Viral Messenger RNA Synthesis / nuclear localization sequence binding / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / macrophage chemotaxis / female gonad development / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / cellular response to nutrient levels / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / positive regulation of TOR signaling / Regulation of HSF1-mediated heat shock response / protein targeting / mRNA transport / regulation of signal transduction / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / 核膜孔 / Mitotic Prometaphase / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / cellular response to amino acid starvation / MHC class II antigen presentation / SH2 domain binding / nuclear periphery / serine-type peptidase activity / SUMOylation of chromatin organization proteins / 神経発生 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
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: 39.0 Å | |||||||||
データ登録者 | Schuller AP / Wojtynek M / Schwartz TU / Medalia O / Weis K | |||||||||
資金援助 | 米国, スイス, 2件
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引用 | ジャーナル: Nature / 年: 2021 タイトル: The cellular environment shapes the nuclear pore complex architecture. 著者: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / ...著者: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / Karsten Weis / Ohad Medalia / Thomas U Schwartz / 要旨: Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about ...Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture. | |||||||||
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
マップデータ | emd_12813.map.gz | 3.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12813-v30.xml emd-12813.xml | 13.2 KB 13.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12813_fsc.xml | 4.7 KB | 表示 | FSCデータファイル |
画像 | emd_12813.png | 37.3 KB | ||
マスクデータ | emd_12813_msk_1.map | 3.8 MB | マスクマップ | |
その他 | emd_12813_half_map_1.map.gz emd_12813_half_map_2.map.gz | 3.5 MB 3.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12813 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12813 | HTTPS FTP |
-関連構造データ
関連構造データ | 7peqC 7perC C: 同じ文献を引用 (文献) |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10700 (タイトル: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-lamella of human DLD-1 cells [tilt series]) EMPIAR-10701 (タイトル: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-milled lamella of Nup96-depleted human DLD-1 cells [tilt series]) |
-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_12813.map.gz / 形式: CCP4 / 大きさ: 3.8 MB / 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: 6.84 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
ファイル | emd_12813_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_12813_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_12813_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Segment of the nucleoplasmic ring of the human nuclear pore complex
全体 | 名称: Segment of the nucleoplasmic ring of the human nuclear pore complex |
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要素 |
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-超分子 #1: Segment of the nucleoplasmic ring of the human nuclear pore complex
超分子 | 名称: Segment of the nucleoplasmic ring of the human nuclear pore complex タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 株: DLD-1 / Organelle: Nuclear envelope / 細胞中の位置: Nuclear envelope |
-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 / 詳細: PBS |
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凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER |
詳細 | Cryo-FIB lamella |
-電子顕微鏡法
顕微鏡 | FEI TITAN 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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 5.0 µm / 最小 デフォーカス(公称値): 2.5 µm / 倍率(公称値): 26000 |
試料ステージ | ホルダー冷却材: NITROGEN |
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: 2.4 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |