+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4crn | ||||||
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タイトル | Cryo-EM of a pretermination complex with eRF1 and eRF3 | ||||||
要素 |
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キーワード | TRANSLATION / TERMINATION / CRYO-EM | ||||||
機能・相同性 | 機能・相同性情報 Eukaryotic Translation Termination / translation release factor complex / cytoplasmic translational termination / translation release factor activity / translation release factor activity, codon specific / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / aminoacyl-tRNA hydrolase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...Eukaryotic Translation Termination / translation release factor complex / cytoplasmic translational termination / translation release factor activity / translation release factor activity, codon specific / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / aminoacyl-tRNA hydrolase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / DNA-templated transcription termination / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / cytoplasmic stress granule / translation / GTPase activity / mRNA binding / GTP binding / identical protein binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | SACCHAROMYCES CEREVISIAE (パン酵母) | ||||||
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: 9.1 Å | ||||||
データ登録者 | Preis, A. / Heuer, A. / Barrio-Garcia, C. / Hauser, A. / Eyler, D. / Berninghausen, O. / Green, R. / Becker, T. / Beckmann, R. | ||||||
引用 | ジャーナル: Cell Rep / 年: 2014 タイトル: Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1. 著者: Anne Preis / Andre Heuer / Clara Barrio-Garcia / Andreas Hauser / Daniel E Eyler / Otto Berninghausen / Rachel Green / Thomas Becker / Roland Beckmann / 要旨: Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and ...Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and guanosine triphosphate (GTP)-bound eRF3. After GTP hydrolysis, eRF3 dissociates, and ABCE1 can bind to eRF1-loaded ribosomes to stimulate peptide release and ribosomal subunit dissociation. Here, we present cryoelectron microscopic (cryo-EM) structures of a pretermination complex containing eRF1-eRF3 and a termination/prerecycling complex containing eRF1-ABCE1. eRF1 undergoes drastic conformational changes: its central domain harboring the catalytically important GGQ loop is either packed against eRF3 or swung toward the peptidyl transferase center when bound to ABCE1. Additionally, in complex with eRF3, the N-terminal domain of eRF1 positions the conserved NIKS motif proximal to the stop codon, supporting its suggested role in decoding, yet it appears to be delocalized in the presence of ABCE1. These results suggest that stop codon decoding and peptide release can be uncoupled during termination. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-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 | 4crn.cif.gz | 166.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4crn.ent.gz | 121.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4crn.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
文書・要旨 | 4crn_validation.pdf.gz | 906.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4crn_full_validation.pdf.gz | 1015.8 KB | 表示 | |
XML形式データ | 4crn_validation.xml.gz | 46.3 KB | 表示 | |
CIF形式データ | 4crn_validation.cif.gz | 63.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crn ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crn | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 47840.965 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: FOR CHAIN P (ERF3) THE FIRST 254 AMINO ACIDS ARE MISSING. 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母) プラスミド: PTYB2 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P05453 |
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#2: タンパク質 | 分子量: 49032.375 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: FOR CHAIN X THE LAST 25 AMINO ACIDS (416-440) ARE MISSING 由来: (組換発現) SACCHAROMYCES CEREVISIAE (パン酵母) プラスミド: PTYB2 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P12385 |
#3: 化合物 | ChemComp-GNP / |
配列の詳細 | THE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS ...THE FIRST 254 AMINO ACIDS FOR THE N-TERMINAL DOMAIN ARE MISSING IN THE MODEL THE LAST AMINO ACIDS (RESIDUES 416-440) ARE MISSING IN THE MODEL |
-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: CMV-STALLED WHEAT GERM 80S-RNC BOUND TO ERF1 AND ABCE1-ADPNP タイプ: RIBOSOME |
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緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: CARBON |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 詳細: LIQUID ETHANE, VITROBOT MARK 4 |
-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 / 日付: 2013年2月20日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(補正後): 147136 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 1300 nm / Cs: 2.7 mm |
撮影 | 電子線照射量: 0.02 e/Å2 フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) |
-解析
EMソフトウェア |
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対称性 | 点対称性: C1 (非対称) | |||||||||||||||
3次元再構成 | 手法: PROJECTION MATCHING / 解像度: 9.1 Å / 粒子像の数: 39309 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2597 (DEPOSITION ID: 12368). 対称性のタイプ: POINT | |||||||||||||||
精密化 | 最高解像度: 9.1 Å | |||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 9.1 Å
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