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基本情報
登録情報 | データベース: PDB / ID: 6i7t | |||||||||||||||
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タイトル | eIF2B:eIF2 complex | |||||||||||||||
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![]() | TRANSLATION / Translational control eIF2 Integrated stress response eIF2B TRANSLATION | |||||||||||||||
機能・相同性 | ![]() negative regulation of cellular response to amino acid starvation / positive regulation of cellular response to heat / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2B complex / : / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex ...negative regulation of cellular response to amino acid starvation / positive regulation of cellular response to heat / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / ABC-family proteins mediated transport / eukaryotic translation initiation factor 2B complex / : / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 2 complex / multi-eIF complex / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of translation preinitiation complex / guanyl-nucleotide exchange factor complex / positive regulation of cellular response to amino acid starvation / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of translational initiation / enzyme regulator activity / translation initiation factor binding / translation initiation factor activity / guanyl-nucleotide exchange factor activity / translational initiation / cytoplasmic stress granule / ribosome binding / ribosome / GTPase activity / mRNA binding / GTP binding / mitochondrion / RNA binding / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||||||||
生物種 | ![]() ![]() | |||||||||||||||
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: 4.61 Å | |||||||||||||||
![]() | Adomavicius, T. / Guaita, M. / Roseman, A.M. / Pavitt, G.D. | |||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: The structural basis of translational control by eIF2 phosphorylation. 著者: Tomas Adomavicius / Margherita Guaita / Yu Zhou / Martin D Jennings / Zakia Latif / Alan M Roseman / Graham D Pavitt / ![]() ![]() 要旨: Protein synthesis in eukaryotes is controlled by signals and stresses via a common pathway, called the integrated stress response (ISR). Phosphorylation of the translation initiation factor eIF2 ...Protein synthesis in eukaryotes is controlled by signals and stresses via a common pathway, called the integrated stress response (ISR). Phosphorylation of the translation initiation factor eIF2 alpha at a conserved serine residue mediates translational control at the ISR core. To provide insight into the mechanism of translational control we have determined the structures of eIF2 both in phosphorylated and unphosphorylated forms bound with its nucleotide exchange factor eIF2B by electron cryomicroscopy. The structures reveal that eIF2 undergoes large rearrangements to promote binding of eIF2α to the regulatory core of eIF2B comprised of the eIF2B alpha, beta and delta subunits. Only minor differences are observed between eIF2 and eIF2αP binding to eIF2B, suggesting that the higher affinity of eIF2αP for eIF2B drives translational control. We present a model for controlled nucleotide exchange and initiator tRNA binding to the eIF2/eIF2B complex. #1: ジャーナル: Elife / 年: 2017 タイトル: Fail-safe control of translation initiation by dissociation of eIF2α phosphorylated ternary complexes. 著者: Martin D Jennings / Christopher J Kershaw / Tomas Adomavicius / Graham D Pavitt / ![]() 要旨: Phosphorylation of eIF2α controls translation initiation by restricting the levels of active eIF2-GTP/Met-tRNAi ternary complexes (TC). This modulates the expression of all eukaryotic mRNAs and ...Phosphorylation of eIF2α controls translation initiation by restricting the levels of active eIF2-GTP/Met-tRNAi ternary complexes (TC). This modulates the expression of all eukaryotic mRNAs and contributes to the cellular integrated stress response. Key to controlling the activity of eIF2 are translation factors eIF2B and eIF5, thought to primarily function with eIF2-GDP and TC respectively. Using a steady-state kinetics approach with purified proteins we demonstrate that eIF2B binds to eIF2 with equal affinity irrespective of the presence or absence of competing guanine nucleotides. We show that eIF2B can compete with Met-tRNAi for eIF2-GTP and can destabilize TC. When TC is formed with unphosphorylated eIF2, eIF5 can out-compete eIF2B to stabilize TC/eIF5 complexes. However when TC/eIF5 is formed with phosphorylated eIF2, eIF2B outcompetes eIF5 and destabilizes TC. These data uncover competition between eIF2B and eIF5 for TC and identify that phosphorylated eIF2-GTP translation initiation intermediate complexes can be inhibited by eIF2B. | |||||||||||||||
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構造の表示
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 848 KB | 表示 | ![]() |
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PDB形式 | ![]() | 666.7 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-Translation initiation factor eIF-2B subunit ... , 5種, 10分子 ABCDEFGHIJ
#1: タンパク質 | 分子量: 34062.027 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: GCN3, AAS2, TIF221, YKR026C / 発現宿主: ![]() ![]() #2: タンパク質 | 分子量: 70945.195 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: GCD2, TIF224, YGR083C / 発現宿主: ![]() ![]() #3: タンパク質 | 分子量: 42621.441 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: GCD7, TIF222, YLR291C, L8003.17 / 発現宿主: ![]() ![]() #4: タンパク質 | 分子量: 81249.062 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: GCD6, TIF225, YDR211W, YD8142.12, YD8142B.03 / 発現宿主: ![]() ![]() #5: タンパク質 | 分子量: 65768.320 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: GCD1, TIF223, TRA3, YOR260W / 発現宿主: ![]() ![]() |
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-Eukaryotic translation initiation factor 2 subunit ... , 3種, 6分子 KLMNOP
#6: タンパク質 | 分子量: 34763.652 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: SUI2, TIF211, YJR007W, J1429 / 発現宿主: ![]() ![]() #7: タンパク質 | 分子量: 31631.309 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: SUI3, TIF212, YPL237W / 発現宿主: ![]() ![]() #8: タンパク質 | 分子量: 57942.699 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: GCD11, TIF213, YER025W / 発現宿主: ![]() ![]() |
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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 |
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試料調製
構成要素 | 名称: Complex of translation initiation factors eIF2 and eIF2B タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT | ||||||||||||||||||||
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分子量 | 値: 0.838 MDa / 実験値: YES | ||||||||||||||||||||
由来(天然) | 生物種: ![]() ![]() | ||||||||||||||||||||
由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||
緩衝液 | pH: 7.5 詳細: Solutions for sample preparation were made fresh, filter sterilized, and degassed. | ||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.28 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 400 divisions/in. / グリッドのタイプ: Homemade | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 294 K / 詳細: Blot for 1 second before plunging |
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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 / 詳細: Tilt at 35 degrees. |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(補正後): 37313 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1000 nm / Calibrated defocus min: 261 nm / 最大 デフォーカス(補正後): 4601 nm / Cs: 2.7 mm / アライメント法: BASIC |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 10 sec. / 電子線照射量: 1 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 撮影したグリッド数: 1 / 実像数: 2154 詳細: Images were taken with 40, 60 or 100 frames in total. The first 2 frames were discarded in motioncorr2. The stage was tilted by 35 degrees. |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS / エネルギーフィルタースリット幅: 20 eV |
画像スキャン | サンプリングサイズ: 5 µm / 横: 3838 / 縦: 3710 / 動画フレーム数/画像: 100 / 利用したフレーム数/画像: 2-100 |
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解析
EMソフトウェア |
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CTF補正 | 詳細: CTF determination was performed per micrograph initially. After particle picking and initial reconstruction, per particle CTF determination was performed. タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 114390 詳細: 2024 images were selected for particle picking. Initially, 3090 particles were picked manually and used for 2D classification into 20 classes. The best 8 classes (containing 2162 particles) ...詳細: 2024 images were selected for particle picking. Initially, 3090 particles were picked manually and used for 2D classification into 20 classes. The best 8 classes (containing 2162 particles) were selected and used as references for automated particle picking in RELION. Particles on the lacey carbon, not in holes, were manually deleted in RELION, before extraction and further iterative cleaning by classification. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.61 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 23274 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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原子モデル構築 | Source name: PDB / タイプ: experimental model
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