+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4v8z | |||||||||||||||||||||
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タイトル | Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex | |||||||||||||||||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / RIBOSOME INITIATION COMPLEX / INITIATOR FACTOR EIF5B / SINGLE PARTICLE ANALYSIS (単粒子解析法) | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway ...triplex DNA binding / ribosome hibernation / translation elongation factor binding / regulation of translational initiation in response to stress / Platelet degranulation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / eukaryotic 48S preinitiation complex / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / mTORC1-mediated signalling / ribosome-associated ubiquitin-dependent protein catabolic process / ヒドロキシル化 / GDP-dissociation inhibitor activity / regulation of translational initiation / : / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / telomeric DNA binding / mRNA destabilization / MTOR / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / positive regulation of protein kinase activity / rescue of stalled ribosome / translational termination / translation initiation factor binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation repressor activity / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translational initiation / DNA-(apurinic or apyrimidinic site) endonuclease activity / cellular response to amino acid starvation / ribosome assembly / translation initiation factor activity / telomere maintenance / small-subunit processome / protein kinase C binding / cytosolic ribosome assembly / maintenance of translational fidelity / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / protein tag activity / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / リボソーム生合成 / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / リボソーム / structural constituent of ribosome / positive regulation of protein phosphorylation / 翻訳 (生物学) / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / GTPase activity / ubiquitin protein ligase binding / GTP binding 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | SACCHAROMYCES CEREVISIAE (パン酵母) METHANOTHERMOBACTER THERMAUTOTROPHICUS (古細菌) | |||||||||||||||||||||
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: 6.6 Å | |||||||||||||||||||||
データ登録者 | Fernandez, I.S. / Bai, X.C. / Hussain, T. / Kelley, A.C. / Lorsch, J.R. / Ramakrishnan, V. / Scheres, S.H.W. | |||||||||||||||||||||
引用 | ジャーナル: Science / 年: 2013 タイトル: Molecular architecture of a eukaryotic translational initiation complex. 著者: Israel S Fernández / Xiao-Chen Bai / Tanweer Hussain / Ann C Kelley / Jon R Lorsch / V Ramakrishnan / Sjors H W Scheres / 要旨: The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start ...The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes. | |||||||||||||||||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "XA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4v8z.cif.gz | 5.4 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4v8z.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 4v8z.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8z ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8z | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+40S RIBOSOMAL PROTEIN ... , 31種, 31分子 A0A1A2A3A4AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZ
-タンパク質 , 5種, 5分子 A5A6A7BmCV
#6: タンパク質 | 分子量: 16559.258 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P05759 |
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#7: タンパク質 | 分子量: 34841.219 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P38011 |
#8: タンパク質 | 分子量: 29052.369 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P39015 |
#73: タンパク質 | 分子量: 14583.077 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P0CH08 |
#83: タンパク質 | 分子量: 65317.055 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母), (組換発現) METHANOTHERMOBACTER THERMAUTOTROPHICUS (古細菌) 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P39730, UniProt: O26359 |
+60S RIBOSOMAL PROTEIN ... , 40種, 40分子 BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBd...
-60S ACIDIC RIBOSOMAL PROTEIN ... , 3種, 3分子 BqBrBs
#76: タンパク質 | 分子量: 33749.121 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P05317 |
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#77: タンパク質・ペプチド | 分子量: 4017.944 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) |
#78: タンパク質・ペプチド | 分子量: 3932.839 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) |
-RNA鎖 , 6種, 6分子 B2B5B7B8CWCX
#79: RNA鎖 | 分子量: 577937.500 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) |
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#80: RNA鎖 | 分子量: 1097493.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: GenBank: BK006945 |
#81: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: GenBank: AE016820 |
#82: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: GenBank: HQ026735 |
#84: RNA鎖 | 分子量: 24422.475 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) |
#85: RNA鎖 | 分子量: 935.620 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) |
-非ポリマー , 4種, 443分子
#86: 化合物 | ChemComp-ZN / #87: 化合物 | ChemComp-MG / #88: 化合物 | ChemComp-OHX / #89: 化合物 | ChemComp-GCP / | |
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-詳細
配列の詳細 | THESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES. |
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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 |
-試料調製
構成要素 | 名称: RECONSTRUCTION OF 80S- EIF5B-MET-ITRNAMET EUKARYOTIC TRANSLATION INITIATION COMPLEX WITH TRNA IN THE PI-SITE AND タイプ: RIBOSOME |
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緩衝液 | 名称: 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT pH: 7.2 詳細: 3MM HEPES-KOH, 6.6 MM TRIS-ACETATE PH 7.2, 3 MM NH4CL, 6.6 MM NH4- ACETATE, 48 MM K-ACETATE, 4 MM MG-ACETATE, 2.4 MM DTT |
試料 | 濃度: 0.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE 詳細: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 90, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT 2.5 SECONDS BEFORE PLUNGING, |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 / 日付: 2013年1月15日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 59000 X / 倍率(補正後): 79096 X / 最大 デフォーカス(公称値): 3900 nm / 最小 デフォーカス(公称値): 1900 nm / Cs: 2 mm |
試料ホルダ | 温度: 85 K |
撮影 | 電子線照射量: 16 e/Å2 フィルム・検出器のモデル: FEI FALCON I (4k x 4k) |
画像スキャン | デジタル画像の数: 1012 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: EACH PARTICLE | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 6.6 Å / 粒子像の数: 5143 / ピクセルサイズ(実測値): 1.77 Å 倍率補正: CROSS-CORRELATION BETWEEN CRYO-EM MAP AND CRYSTAL STRUCTURE 詳細: USE A NEWLY DEVELOPED STATISTICAL MOVIE PROCESSING APPROACH TO COMPENSATE FOR BEAM-INDUCED MOVEMENT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2422. (DEPOSITION ID: 11817). 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 詳細: METHOD--RIGID-BODY FITTING | ||||||||||||
精密化 | 最高解像度: 6.6 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 6.6 Å
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