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基本情報
登録情報 | データベース: PDB / ID: 8oj5 | ||||||||||||||||||
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タイトル | 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) | ||||||||||||||||||
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![]() | RIBOSOME / ER / UFMylation / recycling | ||||||||||||||||||
機能・相同性 | ![]() UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum ...UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / positive regulation of metallopeptidase activity / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of protein kinase activity by regulation of protein phosphorylation / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / regulation of intracellular estrogen receptor signaling pathway / axial mesoderm development / positive regulation of proteasomal protein catabolic process / negative regulation of formation of translation preinitiation complex / negative regulation of protein serine/threonine kinase activity / ribosomal protein import into nucleus / 90S preribosome assembly / TORC2 complex binding / mitotic G2/M transition checkpoint / 転移酵素; アシル基を移すもの; アミノアシル基を移すもの / GAIT complex / middle ear morphogenesis / cartilage development / regulation of canonical NF-kappaB signal transduction / reticulophagy / cytoplasmic side of rough endoplasmic reticulum membrane / mitogen-activated protein kinase binding / A band / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / negative regulation of ubiquitin protein ligase activity / response to L-glutamate / regulation of neuron differentiation / response to aldosterone / retinal ganglion cell axon guidance / negative regulation of protein import into nucleus / G1 to G0 transition / regulation of cyclin-dependent protein serine/threonine kinase activity / homeostatic process / lung morphogenesis / negative regulation of NF-kappaB transcription factor activity / Protein hydroxylation / male meiosis I / ubiquitin-like protein ligase binding / macrophage chemotaxis / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / NF-kappaB binding / RHOA GTPase cycle / hematopoietic stem cell differentiation / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein targeting / cellular response to interleukin-4 / endomembrane system / cellular response to actinomycin D / positive regulation of autophagy / cytosolic ribosome / rough endoplasmic reticulum / endoplasmic reticulum unfolded protein response / Maturation of protein E / positive regulation of glial cell proliferation / Maturation of protein E / ER Quality Control Compartment (ERQC) / MDM2/MDM4 family protein binding / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of protein ubiquitination / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | ![]() | ||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | ||||||||||||||||||
![]() | Penchev, I. / DaRosa, P.A. / Peter, J.J. / Kulathu, Y. / Becker, T. / Beckmann, R. / Kopito, R. | ||||||||||||||||||
資金援助 | European Union, ![]() ![]() ![]()
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![]() | ![]() タイトル: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. 著者: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / ...著者: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / Roland Beckmann / Ron R Kopito / ![]() ![]() ![]() 要旨: Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that ...Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER). UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane. | ||||||||||||||||||
履歴 |
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構造の表示
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 | ![]() | 3.6 MB | 表示 | ![]() |
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PDB形式 | ![]() | 表示 | ![]() | |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.8 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.8 MB | 表示 | |
XML形式データ | ![]() | 219 KB | 表示 | |
CIF形式データ | ![]() | 383.7 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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要素
-RNA鎖 , 3種, 3分子 578
#1: RNA鎖 | 分子量: 1640166.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#2: RNA鎖 | 分子量: 38998.078 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#3: RNA鎖 | 分子量: 50449.812 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-タンパク質 , 6種, 6分子 ABCDLILm
#4: タンパク質 | 分子量: 89722.203 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: O94874, 転移酵素; アシル基を移すもの; アミノアシル基を移すもの |
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#5: タンパク質 | 分子量: 56977.395 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: CDK5RAP3, IC53, LZAP, MSTP016, OK/SW-cl.114, PP1553 発現宿主: ![]() ![]() |
#6: タンパク質 | 分子量: 35663.840 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#7: タンパク質 | 分子量: 9128.552 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#16: タンパク質 | 分子量: 24552.910 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#45: タンパク質 | 分子量: 14758.394 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
+60S ribosomal protein ... , 40種, 40分子 LALBLCLDLELFLGLHLJLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLf...
-非ポリマー , 2種, 225分子 ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#50: 化合物 | ChemComp-MG / #51: 化合物 | ChemComp-ZN / |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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: 単粒子再構成法 |
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試料調製
構成要素 | 名称: E3-UFM1 complex bound to the 60S ribosome / タイプ: RIBOSOME / Entity ID: #1-#49 / 由来: NATURAL |
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分子量 | 実験値: NO |
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 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: 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): 2000 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 50 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
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 2.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 35935 / 対称性のタイプ: POINT |
原子モデル構築 | プロトコル: AB INITIO MODEL |