+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12814 | |||||||||
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タイトル | In-cell 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 GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / Seh1-associated complex / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum ...GATOR2 complex / nephron development / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / Seh1-associated complex / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nuclear envelope organization / nuclear pore central transport channel / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / atrial cardiac muscle cell action potential / nuclear pore organization / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / positive regulation of protein localization to centrosome / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / paraxial mesoderm development / nuclear pore nuclear basket / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / Transport of the SLBP independent Mature mRNA / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / negative regulation of Ras protein signal transduction / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Flemming body / Nuclear import of Rev protein / Transport of Mature mRNA derived from an Intron-Containing Transcript / negative regulation of programmed cell death / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / mitotic centrosome separation / RNA export from nucleus / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / neural tube development / COPII-mediated vesicle transport / Viral Messenger RNA Synthesis / lamellipodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / female gonad development / SUMOylation of ubiquitinylation proteins / negative regulation of epidermal growth factor receptor signaling pathway / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / 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 / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / regulation of signal transduction / mRNA transport / protein targeting / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / Hsp70 protein binding / MHC class II antigen presentation / cellular response to amino acid starvation / serine-type peptidase activity / SUMOylation of chromatin organization proteins / SH2 domain binding / positive regulation of mitotic nuclear division / nuclear periphery 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: 35.0 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_12814.map.gz | 16.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12814-v30.xml emd-12814.xml | 9.6 KB 9.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_12814.png | 60.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12814 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12814_validation.pdf.gz | 304.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12814_full_validation.pdf.gz | 303.7 KB | 表示 | |
XML形式データ | emd_12814_validation.xml.gz | 6.2 KB | 表示 | |
CIF形式データ | emd_12814_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-12814 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12814 | HTTPS FTP |
-関連構造データ
関連構造データ | 7peqMC 7perMC 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 | |
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_12814.map.gz / 形式: CCP4 / 大きさ: 125 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
-試料の構成要素
-全体 : In-cell human nuclear pore complex
全体 | 名称: In-cell human nuclear pore complex |
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要素 |
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-超分子 #1: In-cell human nuclear pore complex
超分子 | 名称: In-cell 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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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 |
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 / 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 |
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: C8 (8回回転対称) / 解像度のタイプ: BY AUTHOR / 解像度: 35.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 使用したサブトモグラム数: 1254 |
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抽出 | トモグラム数: 54 / 使用した粒子像数: 1552 |
最終 角度割当 | タイプ: OTHER |