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基本情報
登録情報 | データベース: PDB / ID: 7peq | ||||||||||||
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タイトル | Model of the outer rings of the human nuclear pore complex | ||||||||||||
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![]() | TRANSPORT PROTEIN / Nuclear Pore Complex / NPC | ||||||||||||
機能・相同性 | ![]() GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery ...GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Transport of Ribonucleoproteins into the Host Nucleus / Amino acids regulate mTORC1 / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / lamellipodium assembly / neural tube development / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / female gonad development / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / 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 / mRNA transport / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / cellular response to nutrient levels / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / negative regulation of TORC1 signaling / neurogenesis / Mitotic Prometaphase / serine-type peptidase activity / positive regulation of TORC1 signaling / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / nuclear periphery / cellular response to amino acid starvation / Resolution of Sister Chromatid Cohesion / SUMOylation of chromatin organization proteins / HCMV Late Events / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / chromosome segregation / intracellular protein transport / Transcriptional regulation by small RNAs / promoter-specific chromatin binding / RHO GTPases Activate Formins / ER to Golgi transport vesicle membrane / molecular condensate scaffold activity / kinetochore / ISG15 antiviral mechanism / spindle / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / protein transport / actin cytoskeleton / snRNP Assembly / nuclear membrane / transcription coactivator activity / defense response to Gram-positive bacterium / nuclear speck / nuclear body / ciliary basal body / ribonucleoprotein complex / lysosomal membrane 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 35 Å | ||||||||||||
![]() | Schuller, A.P. / Wojtynek, M. / Mankus, D. / Tatli, M. / Kronenberg-Tenga, R. / Regmi, S.G. / Dasso, M. / Weis, K. / Medalia, O. / Schwartz, T.U. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() 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 |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 2.5 MB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 981.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 313.3 KB | 表示 | |
CIF形式データ | ![]() | 548.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 12814MC ![]() 7perC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 8.0 Data #1: Un-aligned tilt series of FIB-lamella of human DLD-1 cells [tilt series]) ![]() Data size: 8.0 Data #1: Un-aligned tilt series of FIB-milled lamella of Nup96-depleted human DLD-1 cells [tilt series]) |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-Nuclear pore complex protein ... , 5種, 20分子 ACBCCCDCADBDCDDDAEBECEDEAHBHCHDHAJBJCJDJ
#1: タンパク質 | 分子量: 129108.461 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #2: タンパク質 | 分子量: 106504.969 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: タンパク質 | 分子量: 106039.656 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #6: タンパク質 | 分子量: 75105.266 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #8: タンパク質 | 分子量: 162280.203 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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-タンパク質 , 4種, 16分子 AFBFCFDFAGBGCGDGAIBICIDIAKBKCKDK
#4: タンパク質 | 分子量: 35578.438 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #5: タンパク質 | 分子量: 39700.566 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #7: タンパク質 | 分子量: 42195.652 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() #9: タンパク質 | 分子量: 36748.512 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: CELL / 3次元再構成法: サブトモグラム平均法 |
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試料調製
構成要素 | 名称: Nup96::Neon-AID DLD-1 / タイプ: CELL / Entity ID: all / 由来: NATURAL |
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由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: cryo-FIB milled sections of DLD1 cells |
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 詳細: Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane. |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 2500 nm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 2.4 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||
対称性 | 点対称性: C8 (8回回転対称) | ||||||||||||
3次元再構成 | 解像度: 35 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 1252 / アルゴリズム: BACK PROJECTION / 対称性のタイプ: POINT | ||||||||||||
EM volume selection | Num. of tomograms: 54 / Num. of volumes extracted: 1552 | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT | ||||||||||||
原子モデル構築 | PDB-ID: 5A9Q Accession code: 5A9Q / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 交差検証法: THROUGHOUT | ||||||||||||
原子変位パラメータ | Biso max: 78.15 Å2 / Biso mean: 0.9902 Å2 / Biso min: 0 Å2 |