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基本情報
登録情報 | データベース: PDB / ID: 6sxo | ||||||
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タイトル | Cryo-EM structure of the human Ebp1-ribosome complex | ||||||
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![]() | RIBOSOME / Human Ebp1 / PA2G4 family / MET-AP homolog / expansion segment ES27L | ||||||
機能・相同性 | ![]() eukaryotic 80S initiation complex / axial mesoderm development / 90S preribosome assembly / TORC2 complex binding / middle ear morphogenesis / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Peptide chain elongation / Selenocysteine synthesis ...eukaryotic 80S initiation complex / axial mesoderm development / 90S preribosome assembly / TORC2 complex binding / middle ear morphogenesis / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / 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) / ossification / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / skeletal system development / positive regulation of translation / positive regulation of cell differentiation / sensory perception of sound / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / rRNA processing / transcription corepressor activity / cellular response to UV / azurophil granule lumen / regulation of translation / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / rRNA binding / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / ubiquitin protein ligase binding / synapse / Neutrophil degranulation / negative regulation of apoptotic process / nucleolus / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol 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: 3.3 Å | ||||||
![]() | Wild, K. / Aleksic, M. / Pfeffer, M. / Sinning, I. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. 著者: Klemens Wild / Milan Aleksić / Karine Lapouge / Keven D Juaire / Dirk Flemming / Stefan Pfeffer / Irmgard Sinning / ![]() 要旨: Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature ...Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit. | ||||||
履歴 |
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 1種, 1分子 A
#1: タンパク質 | 分子量: 43851.879 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-60S ribosomal protein ... , 5種, 5分子 LhLkLRLXLY
#2: タンパク質 | 分子量: 14593.624 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#3: タンパク質 | 分子量: 8238.948 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#4: タンパク質 | 分子量: 23535.281 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#5: タンパク質 | 分子量: 17740.193 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#6: タンパク質 | 分子量: 17303.363 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-RNA鎖 , 2種, 2分子 L5L8
#7: RNA鎖 | 分子量: 1640222.125 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#8: RNA鎖 | 分子量: 50449.812 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-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 |
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分子量 | 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||||||||||
緩衝液成分 | 名称: KOAc / 式: MgOAc2 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: 100 nM ribosome, 800 nM Ebp1 | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 293 K |
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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): 3000 nm / 最小 デフォーカス(公称値): 500 nm / Cs: 2.7 mm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 38 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 3370 |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
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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 AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 34467 詳細: Ebp1-60S density segment after 2-body multibody refinement; filtered to global resolution 対称性のタイプ: POINT |