+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4745 | |||||||||
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タイトル | Structure of XBP1u-paused ribosome nascent chain complex with Sec61. | |||||||||
マップデータ | Structure of XBP1u-paused ribosome nascent chain complex with Sec61. | |||||||||
試料 |
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キーワード | translational pausing / XBP1 / UPR / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 ATF6-mediated unfolded protein response / organelle organization / positive regulation of protein acetylation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of vascular wound healing / response to insulin-like growth factor stimulus / sterol homeostasis / positive regulation of lactation / IRE1alpha activates chaperones ...ATF6-mediated unfolded protein response / organelle organization / positive regulation of protein acetylation / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of vascular wound healing / response to insulin-like growth factor stimulus / sterol homeostasis / positive regulation of lactation / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of plasma cell differentiation / endoplasmic reticulum Sec complex / pronephric nephron development / positive regulation of phospholipid biosynthetic process / positive regulation of ERAD pathway / negative regulation of myotube differentiation / intracellular triglyceride homeostasis / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / cellular response to fructose stimulus / protein insertion into ER membrane / XBP1(S) activates chaperone genes / cellular response to laminar fluid shear stress / SRP-dependent cotranslational protein targeting to membrane, translocation / cellular response to nutrient / negative regulation of endoplasmic reticulum unfolded protein response / positive regulation of endothelial cell apoptotic process / positive regulation of endoplasmic reticulum unfolded protein response / cellular response to fluid shear stress / signal sequence binding / post-translational protein targeting to membrane, translocation / positive regulation of MHC class II biosynthetic process / positive regulation of vascular associated smooth muscle cell migration / positive regulation of hepatocyte proliferation / endothelial cell proliferation / cellular response to peptide hormone stimulus / muscle organ development / regulation of G1 to G0 transition / positive regulation of T cell differentiation / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / positive regulation of immunoglobulin production / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / positive regulation of B cell differentiation / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / negative regulation of SMAD protein signal transduction / activation-induced cell death of T cells / IRE1-mediated unfolded protein response / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / protein transmembrane transporter activity / 90S preribosome / positive regulation of TOR signaling / neuron development / cellular response to vascular endothelial growth factor stimulus / TOR signaling / positive regulation of fat cell differentiation / T cell proliferation involved in immune response / fatty acid homeostasis / adipose tissue development / cellular response to interleukin-4 / cis-regulatory region sequence-specific DNA binding / vascular endothelial growth factor receptor signaling pathway / erythrocyte development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ribosomal small subunit export from nucleus / positive regulation of autophagy / cellular response to glucose starvation / translation regulator activity / rough endoplasmic reticulum / endoplasmic reticulum unfolded protein response / ERAD pathway / positive regulation of vascular associated smooth muscle cell proliferation / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / response to endoplasmic reticulum stress / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / phosphatidylinositol 3-kinase/protein kinase B signal transduction / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / ribosomal large subunit biogenesis / liver development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cholesterol homeostasis 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Homo sapiens (ヒト) / Saccharomyces cerevisiae (パン酵母) / Canis lupus familiaris (イヌ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Shanmuganathan V / Cheng J | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Elife / 年: 2019 タイトル: Structural and mutational analysis of the ribosome-arresting human XBP1u. 著者: Vivekanandan Shanmuganathan / Nina Schiller / Anastasia Magoulopoulou / Jingdong Cheng / Katharina Braunger / Florian Cymer / Otto Berninghausen / Birgitta Beatrix / Kenji Kohno / Gunnar von ...著者: Vivekanandan Shanmuganathan / Nina Schiller / Anastasia Magoulopoulou / Jingdong Cheng / Katharina Braunger / Florian Cymer / Otto Berninghausen / Birgitta Beatrix / Kenji Kohno / Gunnar von Heijne / Roland Beckmann / 要旨: XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM ...XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 Å cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_4745.map.gz | 23.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4745-v30.xml emd-4745.xml | 111.9 KB 111.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4745_fsc.xml | 16 KB | 表示 | FSCデータファイル |
画像 | emd_4745.png | 220.3 KB | ||
Filedesc metadata | emd-4745.cif.gz | 20 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4745 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4745 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4745_validation.pdf.gz | 293.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4745_full_validation.pdf.gz | 293 KB | 表示 | |
XML形式データ | emd_4745_validation.xml.gz | 14.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4745 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4745 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_4745.map.gz / 形式: CCP4 / 大きさ: 236.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Structure of XBP1u-paused ribosome nascent chain complex with Sec61. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
+超分子 #1: Structure of XBP1u-paused ribosome nascent chain complex with Sec61.
+超分子 #2: Ribosome
+超分子 #3: X-box-binding protein 1
+超分子 #4: tRNA
+超分子 #5: Sec61
+超分子 #6: mRNA
+分子 #1: 40S ribosomal protein S30
+分子 #2: 40S ribosomal protein S7
+分子 #3: 40S ribosomal protein S8
+分子 #4: Ribosomal protein S9 (Predicted)
+分子 #5: Ribosomal protein S11
+分子 #6: Ribosomal protein S28
+分子 #7: uS10
+分子 #8: eS21
+分子 #9: uS13
+分子 #10: 40S ribosomal protein S27
+分子 #11: eS17
+分子 #12: eS26
+分子 #13: uS11
+分子 #14: eS31
+分子 #15: X-box-binding protein 1
+分子 #20: ribosomal protein RACK1
+分子 #23: uS14
+分子 #24: eS24
+分子 #25: ribosomal protein eS25
+分子 #26: eS19
+分子 #27: ribosomal protein uS15
+分子 #28: 40S ribosomal protein S12
+分子 #29: uL2
+分子 #30: uL3
+分子 #31: uL4
+分子 #32: 60S ribosomal protein L5
+分子 #33: 60S ribosomal protein L6
+分子 #34: uL30
+分子 #35: eL8
+分子 #36: uL6
+分子 #37: Ribosomal protein L10 (Predicted)
+分子 #38: Ribosomal protein L11
+分子 #40: 60S ribosomal protein L13
+分子 #41: Ribosomal protein L14
+分子 #42: Ribosomal protein L15
+分子 #43: uL13
+分子 #44: uL22
+分子 #45: eL18
+分子 #46: eL19
+分子 #47: eL20
+分子 #48: eL21
+分子 #49: eL22
+分子 #50: eL14
+分子 #51: Ribosomal protein L24
+分子 #52: uL23
+分子 #53: Ribosomal protein L26
+分子 #54: 60S ribosomal protein L27
+分子 #55: eS10
+分子 #56: uL15
+分子 #57: eL29
+分子 #58: eL30
+分子 #59: eL31
+分子 #60: eL32
+分子 #61: eL33
+分子 #62: eL34
+分子 #63: uL29
+分子 #64: 60S ribosomal protein L36
+分子 #65: Ribosomal protein L37
+分子 #66: eL38
+分子 #67: eL39
+分子 #68: eL40
+分子 #69: 60s ribosomal protein l41
+分子 #70: eL42
+分子 #71: ribosomal protein eL43
+分子 #72: uS2
+分子 #73: eL28
+分子 #74: 60S acidic ribosomal protein P0
+分子 #75: uL11
+分子 #76: 40S ribosomal protein S3a
+分子 #77: uS5
+分子 #78: Ribosomal protein S3
+分子 #79: 40S ribosomal protein S4
+分子 #80: Ribosomal protein S5
+分子 #81: 40S ribosomal protein S6
+分子 #82: Ribosomal protein S15a
+分子 #83: Ribosomal protein S16
+分子 #84: Ribosomal protein S23
+分子 #85: uS19
+分子 #86: Protein transport protein Sec61 subunit alpha isoform 1
+分子 #87: Protein transport protein Sec61 subunit gamma
+分子 #88: Protein transport protein Sec61 subunit beta
+分子 #16: P-tRNA
+分子 #17: E-tRNA
+分子 #18: messenger RNA
+分子 #19: 28S ribosomal RNA
+分子 #21: 5S ribosomal RNA
+分子 #22: 5.8S ribosomal RNA
+分子 #39: 18S ribosomal RNA
+分子 #89: ZINC ION
+分子 #90: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 28.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-6r7q: |