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基本情報
登録情報 | データベース: EMDB / ID: EMD-3146 | |||||||||
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タイトル | Mechanism of eIF6 release from the nascent 60S ribosomal subunit | |||||||||
![]() | Reconstruction of 60S-eIF6-SBDS-EFL1 complex | |||||||||
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![]() | ribosome / ribosomopathy / SBDS / cryo-EM / eIF6 / Dictyostelium / EFL1 / GTPase / ribosome biogenesis | |||||||||
機能・相同性 | ![]() Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / SRP-dependent cotranslational protein targeting to membrane ...Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC-Cdc20 mediated degradation of Nek2A / SRP-dependent cotranslational protein targeting to membrane / Separation of Sister Chromatids / Senescence-Associated Secretory Phenotype (SASP) / Autodegradation of the E3 ubiquitin ligase COP1 / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / Degradation of DVL / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Hedgehog 'on' state / Translesion synthesis by POLK / Regulation of RAS by GAPs / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Ub-specific processing proteases / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / Regulation of PTEN stability and activity / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Peroxisomal protein import / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / KEAP1-NFE2L2 pathway / Regulation of NF-kappa B signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Regulation of pyruvate metabolism / Orc1 removal from chromatin / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Neddylation / Iron uptake and transport / Antigen processing: Ubiquitination & Proteasome degradation / Aggrephagy / Regulation of necroptotic cell death / leukocyte chemotaxis / GTP metabolic process / bone marrow development / inner cell mass cell proliferation / maturation of 5.8S rRNA / bone mineralization / ribosomal large subunit binding / preribosome, large subunit precursor / translation elongation factor activity / hematopoietic progenitor cell differentiation / ribosomal subunit export from nucleus / phagocytic vesicle / translation initiation factor activity / maturation of LSU-rRNA / extracellular matrix / lipid droplet / mitotic spindle organization / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / spindle pole / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / large ribosomal subunit rRNA binding / microtubule binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å | |||||||||
![]() | Weis F / Giudice E / Churcher M / Jin L / Hilcenko C / Wong CC / Traynor D / Kay RR / Warren AJ | |||||||||
![]() | ![]() タイトル: Mechanism of eIF6 release from the nascent 60S ribosomal subunit. 著者: Félix Weis / Emmanuel Giudice / Mark Churcher / Li Jin / Christine Hilcenko / Chi C Wong / David Traynor / Robert R Kay / Alan J Warren / ![]() ![]() 要旨: SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by ...SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias. | |||||||||
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 | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 14.3 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 14 KB 14 KB | 表示 表示 | ![]() |
画像 | ![]() | 270 KB | ||
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-関連構造データ
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of 60S-eIF6-SBDS-EFL1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : Dictyostelium 60S carrying endogenous eIF6 with recombinant human...
全体 | 名称: Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1 |
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要素 |
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-超分子 #1000: Dictyostelium 60S carrying endogenous eIF6 with recombinant human...
超分子 | 名称: Dictyostelium 60S carrying endogenous eIF6 with recombinant human SBDS and human EFL1 タイプ: sample / ID: 1000 / Number unique components: 4 |
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-超分子 #1: 60S ribosomal subunit
超分子 | 名称: 60S ribosomal subunit / タイプ: complex / ID: 1 / 組換発現: No / Ribosome-details: ribosome-eukaryote: LSU 60S |
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由来(天然) | 生物種: ![]() ![]() 株: HM2917 / 別称: Slime Mold |
分子量 | 実験値: 3 MDa / 理論値: 3 MDa |
-分子 #1: Eukaryotic translation initiation factor 6
分子 | 名称: Eukaryotic translation initiation factor 6 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: eIF6 詳細: endogenous dictyostelium protein purified bound the 60S ribosomal subunit コピー数: 1 / 組換発現: No |
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由来(天然) | 生物種: ![]() ![]() 株: HM2917 / 別称: Slime Mold |
分子量 | 実験値: 26 KDa / 理論値: 26 KDa |
配列 | UniProtKB: Eukaryotic translation initiation factor 6 |
-分子 #2: Shwachman-Bodian-Diamond syndrome protein
分子 | 名称: Shwachman-Bodian-Diamond syndrome protein / タイプ: protein_or_peptide / ID: 2 / Name.synonym: SBDS / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 実験値: 29 KDa / 理論値: 29 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | UniProtKB: Ribosome maturation protein SBDS |
-分子 #3: Elongation factor-like 1
分子 | 名称: Elongation factor-like 1 / タイプ: protein_or_peptide / ID: 3 / Name.synonym: EFL1 / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 実験値: 125 KDa / 理論値: 125 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | UniProtKB: Elongation factor-like GTPase 1 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 詳細: 50 mM HEPES-KOH, 100 mM K(CH3COO), 10 mM Mg(CH3COO)2, 6 mM beta-mercaptoethanol |
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グリッド | 詳細: quantifoil R2/2 glow discharged |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 120 K / 装置: FEI VITROBOT MARK III / 手法: 6.5s blot |
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電子顕微鏡法 #1
Microscopy ID | 1 |
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顕微鏡 | FEI TITAN KRIOS |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 59,000 times magnification |
日付 | 2013年9月3日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 3844 / 平均電子線量: 30 e/Å2 詳細: Every image is the average of 16 frames recorded by the direct electron detector |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 105263 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.2 mm / 最大 デフォーカス(公称値): 2.8 µm / 最小 デフォーカス(公称値): 2.2 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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電子顕微鏡法 #2
Microscopy ID | 2 |
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顕微鏡 | FEI TITAN KRIOS |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 59,000 times magnification |
日付 | 2013年9月6日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 3844 / 平均電子線量: 30 e/Å2 詳細: Every image is the average of 16 frames recorded by the direct electron detector |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 105263 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.2 mm / 最大 デフォーカス(公称値): 2.8 µm / 最小 デフォーカス(公称値): 2.2 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
CTF補正 | 詳細: Each particle |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: RELION / 使用した粒子像数: 11970 |