+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5a9q | ||||||
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タイトル | Human nuclear pore complex | ||||||
要素 |
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キーワード | TRANSPORT PROTEIN | ||||||
機能・相同性 | 機能・相同性情報 GATOR2 complex / nephron development / Seh1-associated complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nuclear envelope organization / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...GATOR2 complex / nephron development / Seh1-associated complex / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nuclear envelope organization / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / atrial cardiac muscle cell action potential / nuclear pore organization / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / 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 / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / 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 / nucleocytoplasmic transport / neural tube development / COPII-mediated vesicle transport / positive regulation of mRNA splicing, via spliceosome / lamellipodium assembly / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / female gonad development / SUMOylation of ubiquitinylation proteins / 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 / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / cellular response to nutrient levels / mRNA transport / 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 / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / cellular response to amino acid starvation / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / neurogenesis / molecular condensate scaffold activity / HCMV Late Events / chromosome segregation / RHO GTPases Activate Formins / promoter-specific chromatin binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Transcriptional regulation by small RNAs / intracellular protein transport / ER to Golgi transport vesicle membrane / kinetochore / ISG15 antiviral mechanism / HCMV Early Events / spindle / protein import into nucleus / Separation of Sister Chromatids / protein transport / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / defense response to Gram-positive bacterium 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) | ||||||
手法 | 電子顕微鏡法 / 電子線トモグラフィー法 / クライオ電子顕微鏡法 / 解像度: 23 Å | ||||||
データ登録者 | von Appen, A. / Kosinski, J. / Sparks, L. / Ori, A. / DiGuilio, A. / Vollmer, B. / Mackmull, M. / Banterle, N. / Parca, L. / Kastritis, P. ...von Appen, A. / Kosinski, J. / Sparks, L. / Ori, A. / DiGuilio, A. / Vollmer, B. / Mackmull, M. / Banterle, N. / Parca, L. / Kastritis, P. / Buczak, K. / Mosalaganti, S. / Hagen, W. / Andres-Pons, A. / Lemke, E.A. / Bork, P. / Antonin, W. / Glavy, J.S. / Bui, K.H. / Beck, M. | ||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: In situ structural analysis of the human nuclear pore complex. 著者: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / ...著者: Alexander von Appen / Jan Kosinski / Lenore Sparks / Alessandro Ori / Amanda L DiGuilio / Benjamin Vollmer / Marie-Therese Mackmull / Niccolo Banterle / Luca Parca / Panagiotis Kastritis / Katarzyna Buczak / Shyamal Mosalaganti / Wim Hagen / Amparo Andres-Pons / Edward A Lemke / Peer Bork / Wolfram Antonin / Joseph S Glavy / Khanh Huy Bui / Martin Beck / 要旨: Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and ...Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5a9q.cif.gz | 2.7 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5a9q.ent.gz | 1.7 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5a9q.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 5a9q_validation.pdf.gz | 941.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5a9q_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | 5a9q_validation.xml.gz | 349.2 KB | 表示 | |
CIF形式データ | 5a9q_validation.cif.gz | 612.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/a9/5a9q ftp://data.pdbj.org/pub/pdb/validation_reports/a9/5a9q | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
-タンパク質 , 4種, 16分子 09IR2KTb6FOX7GPY
#1: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: Q8NFH3 #3: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: Q8NFH4 #7: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: P55735 #8: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: Q96EE3 |
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-NUCLEAR PORE COMPLEX PROTEIN ... , 6種, 22分子 1JSa3CLU4DMV5ENW8HQZAB
#2: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: Q12769 #4: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: Q8WUM0 #5: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: P57740 #6: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: P52948 #9: 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) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: Q9BW27 #10: タンパク質 | 分子量: 155357.281 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) HOMO SAPIENS (ヒト) / 細胞株: HELA / 参照: UniProt: O75694 |
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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: PARTICLE / 3次元再構成法: 電子線トモグラフィー法 |
-試料調製
構成要素 | 名称: HUMAN NUCLEAR PORE COMPLEX / タイプ: ORGANELLE OR CELLULAR COMPONENT |
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緩衝液 | 名称: 20MM TRIS, 0.2-0.4% TREHALOSE / pH: 7.5 / 詳細: 20MM TRIS, 0.2-0.4% TREHALOSE |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE-PROPANE 詳細: VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER, |
-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 / 日付: 2014年10月17日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 42000 X / 倍率(補正後): 42000 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 2000 nm / Cs: 2.7 mm |
試料ホルダ | 傾斜角・最大: 60 ° / 傾斜角・最小: -45 ° |
撮影 | 電子線照射量: 110 e/Å2 / フィルム・検出器のモデル: GATAN K2 (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | 詳細: PHASE FLIPPING OF TILT SERIES | ||||||||||||
対称性 | 点対称性: C8 (8回回転対称) | ||||||||||||
3次元再構成 | 手法: SUBTOMOGRAM AVERAGING / 解像度: 23 Å 詳細: THIS PDB STRUCTURE INCLUDES UNAMBIGUOUS FITS ONLY. THE STRUCTURE WITH LESS CONFIDENT FITS CAN BE OBTAINED FROM AUTHORS. PROTEIN-PROTEIN INTERFACES SHALL NOT BE INTERPRETED AT RESIDUE-LEVEL ...詳細: THIS PDB STRUCTURE INCLUDES UNAMBIGUOUS FITS ONLY. THE STRUCTURE WITH LESS CONFIDENT FITS CAN BE OBTAINED FROM AUTHORS. PROTEIN-PROTEIN INTERFACES SHALL NOT BE INTERPRETED AT RESIDUE-LEVEL RESOLUTION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3103. (DEPOSITION ID: 13616). 対称性のタイプ: POINT | ||||||||||||
精密化 | 最高解像度: 23 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 23 Å
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