+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13851 | |||||||||
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タイトル | Cryo-em structure of the Nup98 fibril polymorph 1 | |||||||||
マップデータ | Cryo-em structure of the Nup98 fibril polymorph 1 | |||||||||
試料 |
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キーワード | Nuclear pore complex protein Nup98 functional amyloid fibril PROTEIN FIBRIL / PROTEIN FIBRIL | |||||||||
機能・相同性 | 機能・相同性情報 nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of mRNA splicing, via spliceosome / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / 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 / mRNA transport / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / promoter-specific chromatin binding / RHO GTPases Activate Formins / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 2.76 Å | |||||||||
データ登録者 | Ibanez de Opakua A / Geraets JA | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Nat Chem / 年: 2022 タイトル: Molecular interactions of FG nucleoporin repeats at high resolution. 著者: Alain Ibáñez de Opakua / James A Geraets / Benedikt Frieg / Christian Dienemann / Adriana Savastano / Marija Rankovic / Maria-Sol Cima-Omori / Gunnar F Schröder / Markus Zweckstetter / 要旨: Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear ...Proteins that contain repeat phenylalanine-glycine (FG) residues phase separate into oncogenic transcription factor condensates in malignant leukaemias, form the permeability barrier of the nuclear pore complex and mislocalize in neurodegenerative diseases. Insights into the molecular interactions of FG-repeat nucleoporins have, however, remained largely elusive. Using a combination of NMR spectroscopy and cryoelectron microscopy, we have identified uniformly spaced segments of transient β-structure and a stable preformed α-helix recognized by messenger RNA export factors in the FG-repeat domain of human nucleoporin 98 (Nup98). In addition, we have determined at high resolution the molecular organization of reversible FG-FG interactions in amyloid fibrils formed by a highly aggregation-prone segment in Nup98. We have further demonstrated that amyloid-like aggregates of the FG-repeat domain of Nup98 have low stability and are reversible. Our results provide critical insights into the molecular interactions underlying the self-association and phase separation of FG-repeat nucleoporins in physiological and pathological cell activities. | |||||||||
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_13851.map.gz | 55.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13851-v30.xml emd-13851.xml | 14.7 KB 14.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13851_fsc.xml | 8.9 KB | 表示 | FSCデータファイル |
画像 | emd_13851.png | 119.3 KB | ||
Filedesc metadata | emd-13851.cif.gz | 4.9 KB | ||
その他 | emd_13851_half_map_1.map.gz emd_13851_half_map_2.map.gz | 46.2 MB 46.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13851 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13851 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13851_validation.pdf.gz | 883.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13851_full_validation.pdf.gz | 883.5 KB | 表示 | |
XML形式データ | emd_13851_validation.xml.gz | 14.5 KB | 表示 | |
CIF形式データ | emd_13851_validation.cif.gz | 20.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13851 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13851 | HTTPS FTP |
-関連構造データ
-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_13851.map.gz / 形式: CCP4 / 大きさ: 59.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-em structure of the Nup98 fibril polymorph 1 | ||||||||||||||||||||||||||||||||||||
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: 1.05 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
-ハーフマップ: Cryo-em structure of the Nup98 fibril polymorph 1, half map 2
ファイル | emd_13851_half_map_1.map | ||||||||||||
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注釈 | Cryo-em structure of the Nup98 fibril polymorph 1, half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Cryo-em structure of the Nup98 fibril polymorph 1, half map 1
ファイル | emd_13851_half_map_2.map | ||||||||||||
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注釈 | Cryo-em structure of the Nup98 fibril polymorph 1, half map 1 | ||||||||||||
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 : The nuclear pore complex protein Nup98 fibril polymorph 1
全体 | 名称: The nuclear pore complex protein Nup98 fibril polymorph 1 |
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要素 |
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-超分子 #1: The nuclear pore complex protein Nup98 fibril polymorph 1
超分子 | 名称: The nuclear pore complex protein Nup98 fibril polymorph 1 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: The Nup98 polymorph 1 fibril is formed by three protofilaments, consisting of Nup98 monomers. |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Nuclear pore complex protein Nup98
分子 | 名称: Nuclear pore complex protein Nup98 / タイプ: protein_or_peptide / ID: 1 / コピー数: 30 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 4.005211 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: TGTANTLFGT ASTGTSLFSS QNNAFAQNKP TGFGNFGTST UniProtKB: Nuclear pore complex protein Nup98-Nup96 |
-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 | らせん対称体再構成法 |
試料の集合状態 | filament |
-試料調製
緩衝液 | pH: 7 |
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 293 K / 装置: FEI VITROBOT MARK IV |
-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 (6k x 4k) / 実像数: 4180 / 平均露光時間: 2.557 sec. / 平均電子線量: 41.0 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 / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.0 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm 倍率(公称値): 81000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |