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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 5ijo | ||||||
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タイトル | Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) | ||||||
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![]() | TRANSPORT PROTEIN / Nuclear pore complex / Nucleocytoplasmic transport | ||||||
機能・相同性 | ![]() centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / atrial cardiac muscle cell action potential / nuclear pore organization / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / negative regulation of epidermal growth factor receptor signaling pathway / 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 / 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 / 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 / negative regulation of programmed cell death / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / mitotic centrosome separation / centrosome cycle / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / positive regulation of epidermal growth factor receptor signaling pathway / SUMOylation of chromatin organization proteins / PTB domain binding / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / regulation of signal transduction / mRNA transport / protein targeting / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / regulation of mitotic spindle organization / Hsp70 protein binding / positive regulation of mitotic nuclear division / SH2 domain binding / HCMV Late Events / nuclear periphery / ubiquitin binding / Transcriptional regulation by small RNAs / HCMV Early Events / Hsp90 protein binding / cellular senescence / phospholipid binding / mitotic spindle / ISG15 antiviral mechanism / spindle pole / protein import into nucleus / nuclear envelope / signaling receptor complex adaptor activity / protein transport / positive regulation of canonical NF-kappaB signal transduction / snRNP Assembly / nuclear membrane / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / chromatin binding / centrosome / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / identical protein binding / membrane / cytoplasm / cytosol 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: 21.4 Å | ||||||
![]() | Kosinski, J. / Mosalaganti, S. / von Appen, A. / Beck, M. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Molecular architecture of the inner ring scaffold of the human nuclear pore complex. 著者: Jan Kosinski / Shyamal Mosalaganti / Alexander von Appen / Roman Teimer / Amanda L DiGuilio / William Wan / Khanh Huy Bui / Wim J H Hagen / John A G Briggs / Joseph S Glavy / Ed Hurt / Martin Beck / ![]() ![]() ![]() 要旨: Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these ...Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar. | ||||||
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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ダウンロード
PDBx/mmCIF形式 | ![]() | 2.2 MB | 表示 | ![]() |
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PDB形式 | ![]() | 1.4 MB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.7 MB | 表示 | |
XML形式データ | ![]() | 349.7 KB | 表示 | |
CIF形式データ | ![]() | 561.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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1 | ![]()
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対称性 | 点対称性: (シェーンフリース記号: C8 (8回回転対称)) |
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要素
-Nuclear pore complex protein ... , 3種, 12分子 ABEKQWCIOUDP
#1: タンパク質 | 分子量: 155357.281 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #2: タンパク質 | 分子量: 93599.102 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #3: タンパク質 | 分子量: 228172.875 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
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-タンパク質 , 4種, 14分子 FLRXGMSYHNTZJV
#4: タンパク質 | 分子量: 55491.156 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #5: タンパク質 | 分子量: 60941.480 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #6: タンパク質 | 分子量: 53289.574 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #7: タンパク質 | 分子量: 196256.688 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
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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: サブトモグラム平均法 |
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試料調製
構成要素 | 名称: Nuclear envelope / タイプ: COMPLEX / Entity ID: #1-#8 / 由来: MULTIPLE SOURCES |
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緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE-PROPANE |
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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 |
撮影 | 電子線照射量: 3 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) |
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解析
EMソフトウェア |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / 空間群名: P1 / 空間群番号: 1 | ||||||||||||
CTF補正 | タイプ: PHASE FLIPPING ONLY | ||||||||||||
3次元再構成 | 解像度: 21.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 8400 / 対称性のタイプ: POINT | ||||||||||||
EM volume selection | Num. of tomograms: 101 / Num. of volumes extracted: 1112 | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT 詳細: this pdb structure includes unambiguous fits only, .i.e. excluding the middle domains of nup188 and nup205. the structure with that domains can be obtained from authors. protein-protein ...詳細: this pdb structure includes unambiguous fits only, .i.e. excluding the middle domains of nup188 and nup205. the structure with that domains can be obtained from authors. protein-protein interfaces shall not be interpreted at residue-level resolution. |