+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jap | ||||||
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タイトル | Structure of a partial yeast 48S preinitiation complex in closed conformation | ||||||
要素 |
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キーワード | TRANSLATION / Eukaryotic translation initiation / 48S / small ribosome subunit / 40S / 43S | ||||||
機能・相同性 | 機能・相同性情報 formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / incipient cellular bud site ...formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / incipient cellular bud site / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / 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) / translation initiation factor binding / translation initiation factor activity / 90S preribosome / rescue of stalled ribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational initiation / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / small-subunit processome / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / double-stranded RNA binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / nucleolus / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Saccharomyces cerevisiae (パン酵母) Kluyveromyces lactis (酵母) synthetic construct (人工物) | ||||||
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: 4.9 Å | ||||||
データ登録者 | Llacer, J.L. / Hussain, T. / Ramakrishnan, V. | ||||||
引用 | ジャーナル: Mol Cell / 年: 2015 タイトル: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex. 著者: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan / 要旨: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition. | ||||||
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 | 3jap.cif.gz | 2.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3jap.ent.gz | 1.6 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3jap.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 | 3jap_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3jap_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 3jap_validation.xml.gz | 192 KB | 表示 | |
CIF形式データ | 3jap_validation.cif.gz | 332.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jap ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jap | 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 , 3種, 3分子 123
#1: RNA鎖 | 分子量: 24223.482 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Kluyveromyces lactis (酵母) |
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#2: RNA鎖 | 分子量: 573814.125 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Kluyveromyces lactis (酵母) |
#3: RNA鎖 | 分子量: 7786.572 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
+タンパク質 , 42種, 42分子 ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
-タンパク質・ペプチド , 2種, 2分子 hr
#37: タンパク質・ペプチド | 分子量: 3354.243 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Kluyveromyces lactis (酵母) / 参照: UniProt: P0CX86 |
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#46: タンパク質・ペプチド | 分子量: 3963.560 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) 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P06103 |
-非ポリマー , 4種, 87分子
#48: 化合物 | ChemComp-MG / #49: 化合物 | ChemComp-ZN / #50: 化合物 | ChemComp-MET / | #51: 化合物 | ChemComp-GCP / | |
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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 |
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緩衝液 | 名称: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT pH: 6.5 詳細: 20 mM MES-KOH, 40 mM potassium acetate, 10 mM ammonium acetate, 8 mM magnesium acetate, 2 mM DTT | ||||||||||||||||||||||||||||||||||||
試料 | 濃度: 0.17 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: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top | ||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK I / 凍結剤: ETHANE / Temp: 120 K / 湿度: 100 % 詳細: Blot for 2.5 to 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK I). 手法: Blot for 2.5 to 3 seconds before plunging |
-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: 2014年7月4日 詳細: Complete dataset was collected over two non-consecutive days. |
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 FIELD / 倍率(公称値): 59000 X / 倍率(補正後): 104478 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.7 mm |
試料ホルダ | 資料ホルダタイプ: GATAN LIQUID NITROGEN |
撮影 | 電子線照射量: 27 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | デジタル画像の数: 5500 |
放射波長 | 相対比: 1 |
-解析
ソフトウェア | 名称: REFMAC / バージョン: 5.8.0124 2015/06/03 / 分類: 精密化 / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk 解説: (un)restrained refinement or idealisation of macromolecular structures | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: 4.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 21401 / ピクセルサイズ(公称値): 1.34 Å / ピクセルサイズ(実測値): 1.34 Å / 詳細: gold-standard / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: RECIPROCAL / Target criteria: R-factor, FSC / 詳細: METHOD--Local refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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精密化 | 詳細: Hydrogens have been added in their riding positions | |||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST
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