+データを開く
-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 | |||||||||
マップデータ | Reconstruction of 60S-eIF6-SBDS-EFL1 complex | |||||||||
試料 |
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キーワード | ribosome (リボソーム) / ribosomopathy / SBDS / cryo-EM (低温電子顕微鏡法) / eIF6 / Dictyostelium / EFL1 / GTPase (GTPアーゼ) / ribosome biogenesis (リボソーム生合成) | |||||||||
機能・相同性 | 機能・相同性情報 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) ...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 / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hedgehog ligand biogenesis / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / 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 / : / : / Aggrephagy / 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) / : / 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 / leukocyte chemotaxis / GTP metabolic process / bone marrow development / inner cell mass cell proliferation / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / bone mineralization / ribosomal large subunit binding / preribosome, large subunit precursor / translation elongation factor activity / hematopoietic progenitor cell differentiation / phagocytic vesicle / maturation of LSU-rRNA / ribosomal large subunit biogenesis / 細胞外マトリックス / translation initiation factor activity / lipid droplet / assembly of large subunit precursor of preribosome / mitotic spindle organization / cytosolic ribosome assembly / modification-dependent protein catabolic process / protein tag activity / rRNA processing / 紡錘体 / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / リボソーム生合成 / cytoplasmic translation / cytosolic large ribosomal subunit / microtubule binding / rRNA binding / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / 翻訳 (生物学) / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding 類似検索 - 分子機能 | |||||||||
生物種 | Dictyostelium discoideum (キイロタマホコリカビ) / Homo sapiens (ヒト) | |||||||||
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 | |||||||||
データ登録者 | Weis F / Giudice E / Churcher M / Jin L / Hilcenko C / Wong CC / Traynor D / Kay RR / Warren AJ | |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2015 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 |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_3146.map.gz | 14.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3146-v30.xml emd-3146.xml | 14 KB 14 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3146.jpg | 270 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3146 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3146 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_3146.map.gz / 形式: CCP4 / 大きさ: 100.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-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: Dictyostelium discoideum (キイロタマホコリカビ) 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: Dictyostelium discoideum (キイロタマホコリカビ) 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: Homo sapiens (ヒト) / 別称: Human |
分子量 | 実験値: 29 KDa / 理論値: 29 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) / 組換株: C41 / 組換プラスミド: pRSETA |
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: Homo sapiens (ヒト) / 別称: Human |
分子量 | 実験値: 125 KDa / 理論値: 125 KDa |
組換発現 | 生物種: Saccharomyces cerevisiae (パン酵母) / 組換株: BCY123 / 組換プラスミド: pYES2 |
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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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-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 |
-電子顕微鏡法 #1
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 105263 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / 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 |
Microscopy ID | 1 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-電子顕微鏡法 #2
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 105263 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / 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 |
Microscopy ID | 2 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-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 |