+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5u4j | ||||||
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タイトル | Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome | ||||||
要素 |
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キーワード | RIBOSOME / ArfA / RF2 / nonstop translation | ||||||
機能・相同性 | 機能・相同性情報 translation release factor activity, codon specific / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / positive regulation of RNA splicing ...translation release factor activity, codon specific / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / positive regulation of RNA splicing / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / viral translational frameshifting / translation / response to antibiotic / mRNA binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Escherichia coli (大腸菌) | ||||||
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: 3.7 Å | ||||||
データ登録者 | Zeng, F. / Chen, Y. / Remis, J. / Shekhar, M. / Phillips, J.C. / Tajkhorshid, E. / Jin, H. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2017 タイトル: Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. 著者: Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin / 要旨: Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs ...Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5u4j.cif.gz | 401.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5u4j.ent.gz | 250.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5u4j.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 | 5u4j_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5u4j_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 5u4j_validation.xml.gz | 41.8 KB | 表示 | |
CIF形式データ | 5u4j_validation.cif.gz | 63.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4j ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4j | 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
-RNA鎖 , 4種, 4分子 aAzx
#1: RNA鎖 | 分子量: 497075.812 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: MRE600 / 参照: GenBank: 817573384 |
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#2: RNA鎖 | 分子量: 941790.625 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Escherichia coli (大腸菌) / 株: MRE600 / 参照: GenBank: 42756 |
#6: RNA鎖 | 分子量: 5922.644 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌) |
#7: RNA鎖 | 分子量: 24786.785 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: RNA was prepared by in vitro transcription / 由来: (合成) Escherichia coli (大腸菌) / 参照: GenBank: 687670942 |
-30S ribosomal protein ... , 4種, 4分子 cdel
#3: タンパク質 | 分子量: 26031.316 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Gene Name(s): rpsC b3314 JW3276 / 由来: (天然) Escherichia coli (大腸菌) / 株: MRE600 / 参照: UniProt: P0A7V3 |
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#4: タンパク質 | 分子量: 23514.199 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Gene Name(s): rpsD ramA b3296 JW3258 / 由来: (天然) Escherichia coli (大腸菌) / 株: MRE600 / 参照: UniProt: P0A7V8 |
#5: タンパク質 | 分子量: 17629.398 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Gene Name(s): rpsE spc b3303 JW3265 / 由来: (天然) Escherichia coli (大腸菌) / 株: MRE600 / 参照: UniProt: P0A7W1 |
#8: タンパク質 | 分子量: 13768.157 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: Gene Name(s): rpsL strA b3342 JW3304 / 由来: (天然) Escherichia coli (大腸菌) / 株: MRE600 / 参照: UniProt: P0A7S3 |
-タンパク質 , 2種, 2分子 vw
#9: タンパク質 | 分子量: 43299.844 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Gene Name(s): prfB ECK2886 JW5847 supK / 由来: (組換発現) Escherichia coli (大腸菌) / 株: MRE600 / 遺伝子: prfB, supK, b2891, JW5847 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P07012 |
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#10: タンパク質 | 分子量: 6513.396 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Gene Name(s): arfA ECK3278 JW3253 yhdL / 由来: (組換発現) Escherichia coli (大腸菌) / 株: MRE600 / 遺伝子: arfA, yhdL, b4550, JW3253 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P36675 |
-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 |
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