+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4735 | |||||||||
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タイトル | Structure of XBP1u-paused ribosome nascent chain complex with SRP. | |||||||||
マップデータ | Structure of XBP1u-paused nascent chain complex with SRP. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 ATF6-mediated unfolded protein response / SRP-dependent cotranslational protein targeting to membrane / positive regulation of protein acetylation / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / response to insulin-like growth factor stimulus / endoplasmic reticulum signal peptide binding / positive regulation of vascular wound healing / organelle organization / positive regulation of plasma cell differentiation / signal recognition particle, endoplasmic reticulum targeting ...ATF6-mediated unfolded protein response / SRP-dependent cotranslational protein targeting to membrane / positive regulation of protein acetylation / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / response to insulin-like growth factor stimulus / endoplasmic reticulum signal peptide binding / positive regulation of vascular wound healing / organelle organization / positive regulation of plasma cell differentiation / signal recognition particle, endoplasmic reticulum targeting / positive regulation of lactation / IRE1alpha activates chaperones / sterol homeostasis / ATF6 (ATF6-alpha) activates chaperone genes / positive regulation of ERAD pathway / signal recognition particle binding / granulocyte differentiation / : / positive regulation of phospholipid biosynthetic process / negative regulation of translational elongation / negative regulation of myotube differentiation / intracellular triglyceride homeostasis / signal-recognition-particle GTPase / protein targeting to ER / cellular response to fructose stimulus / XBP1(S) activates chaperone genes / negative regulation of endoplasmic reticulum unfolded protein response / cellular response to laminar fluid shear stress / cellular response to nutrient / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / cellular response to fluid shear stress / positive regulation of endothelial cell apoptotic process / SRP-dependent cotranslational protein targeting to membrane / positive regulation of MHC class II biosynthetic process / positive regulation of endoplasmic reticulum unfolded protein response / positive regulation of vascular associated smooth muscle cell migration / endothelial cell proliferation / positive regulation of hepatocyte proliferation / ERAD pathway / muscle organ development / positive regulation of T cell differentiation / cellular response to peptide hormone stimulus / positive regulation of B cell differentiation / IRE1-mediated unfolded protein response / positive regulation of immunoglobulin production / neuron development / positive regulation of TOR signaling / positive regulation of fat cell differentiation / fatty acid homeostasis / cellular response to vascular endothelial growth factor stimulus / cellular response to glucose starvation / adipose tissue development / ribonucleoprotein complex binding / 小胞体 / cis-regulatory region sequence-specific DNA binding / vascular endothelial growth factor receptor signaling pathway / positive regulation of autophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of vascular associated smooth muscle cell proliferation / response to endoplasmic reticulum stress / cellular response to interleukin-4 / DNA-(apurinic or apyrimidinic site) lyase / cytosolic ribosome / 好中球 / cholesterol homeostasis / liver development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear estrogen receptor binding / regulation of cell growth / cellular response to glucose stimulus / cellular response to amino acid stimulus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of transforming growth factor beta receptor signaling pathway / protein destabilization / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / chromatin DNA binding / オートファジー / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / cellular response to insulin stimulus / fatty acid biosynthetic process / GDP binding / positive regulation of angiogenesis / protein transport / sequence-specific double-stranded DNA binding / large ribosomal subunit / リボソーム生合成 / cellular response to oxidative stress / 5S rRNA binding / cytosolic large ribosomal subunit / ubiquitin-dependent protein catabolic process / 血管新生 / cellular response to lipopolysaccharide / protease binding 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Saccharomyces cerevisiae (パン酵母) / Homo sapiens (ヒト) / Canis lupus familiaris (イヌ) / Rabbit (ウサギ) / Dog (イヌ) / Human (ヒト) / Baker's yeast (パン酵母) | |||||||||
手法 | 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 | Shanmuganathan V / Cheng J / Braunger K / Berninghausen O / Beatrix B / Beckmann R | |||||||||
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_4735.map.gz | 28.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4735-v30.xml emd-4735.xml | 114.4 KB 114.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4735_fsc.xml | 16 KB | 表示 | FSCデータファイル |
画像 | emd_4735.png | 189.4 KB | ||
その他 | emd_4735_additional.map.gz | 222.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4735 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4735 | 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_4735.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 nascent chain complex with SRP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-追加マップ: Structure of XBP1u-paused nascent chain complex with SRP...
ファイル | emd_4735_additional.map | ||||||||||||
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注釈 | Structure of XBP1u-paused nascent chain complex with SRP (lowpass filtered at 6 A) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Structure of XBP1u-paused ribosome nascent chain complex with SRP.
+超分子 #1: Structure of XBP1u-paused ribosome nascent chain complex with SRP.
+超分子 #2: Structure of XBP1u-paused nascent chain complex with SRP.
+超分子 #3: P- and E- site tRNA
+超分子 #4: X-box-binding protein 1
+超分子 #5: mRNA encoding XBP1u
+超分子 #6: SRP
+超分子 #7: Signal sequence (HR2)
+分子 #1: eS31
+分子 #2: X-box-binding protein 1
+分子 #7: ribosomal protein RACK1
+分子 #10: uS14
+分子 #11: uL2
+分子 #12: 40S ribosomal protein S30
+分子 #13: uL3
+分子 #14: 40S ribosomal protein S7
+分子 #15: uL4
+分子 #16: 40S ribosomal protein S8
+分子 #17: Ribosomal protein S9 (Predicted)
+分子 #18: 60S ribosomal protein L5
+分子 #19: Ribosomal protein S11
+分子 #20: 60S ribosomal protein L6
+分子 #21: Ribosomal protein S28
+分子 #22: uL30
+分子 #23: Ribosomal protein S20
+分子 #24: eL8
+分子 #25: uL6
+分子 #26: 40S ribosomal protein S21
+分子 #27: Ribosomal protein L10 (Predicted)
+分子 #28: uS13
+分子 #29: 40S ribosomal protein S27
+分子 #30: Ribosomal protein L11
+分子 #32: eS17
+分子 #33: 60S ribosomal protein L13
+分子 #34: 40S ribosomal protein S26
+分子 #35: Ribosomal protein L14
+分子 #36: 40S ribosomal protein S14
+分子 #37: Ribosomal protein L15
+分子 #38: 40S ribosomal protein S24
+分子 #39: 60S ribosomal protein L13a
+分子 #40: ribosomal protein eS25
+分子 #41: uL22
+分子 #42: eS19
+分子 #43: eL18
+分子 #44: ribosomal protein uS15
+分子 #45: 60S ribosomal protein L19
+分子 #46: 40S ribosomal protein S12
+分子 #47: eL20
+分子 #48: eS10
+分子 #49: eL21
+分子 #50: Ribosomal protein S15a
+分子 #51: Ribosomal protein S16
+分子 #52: 60S ribosomal protein L22
+分子 #53: Ribosomal protein S23
+分子 #54: eL14
+分子 #55: Ribosomal protein L24
+分子 #56: uS19
+分子 #57: uL23
+分子 #58: Ribosomal protein L26
+分子 #59: 60S ribosomal protein L27
+分子 #60: uL15
+分子 #61: eL29
+分子 #62: eL30
+分子 #63: eL31
+分子 #64: eL32
+分子 #65: eL33
+分子 #66: eL34
+分子 #67: uL29
+分子 #68: 60S ribosomal protein L36
+分子 #69: Ribosomal protein L37
+分子 #70: 60S ribosomal protein L38
+分子 #71: eL39
+分子 #72: 60S ribosomal protein L40
+分子 #73: 60s ribosomal protein l41
+分子 #74: eL42
+分子 #75: ribosomal protein eL43
+分子 #76: uS2
+分子 #77: eL28
+分子 #78: 60S acidic ribosomal protein P0
+分子 #79: uL11
+分子 #80: 40S ribosomal protein S3a
+分子 #81: uS5
+分子 #82: Ribosomal protein S3
+分子 #83: 40S ribosomal protein S4
+分子 #84: Ribosomal protein S5
+分子 #85: 40S ribosomal protein S6
+分子 #86: Signal recognition particle 54 kDa protein
+分子 #88: Signal recognition particle subunit SRP19
+分子 #89: Signal recognition particle subunit SRP68
+分子 #90: Signal recognition particle 9 kDa protein
+分子 #91: Signal recognition particle 14 kDa protein
+分子 #92: Signal sequence (HR2)
+分子 #3: P-tRNA
+分子 #4: E-tRNA
+分子 #5: mRNA
+分子 #6: 28S ribosomal RNA
+分子 #8: 5S ribosomal RNA
+分子 #9: 5.8S ribosomal RNA
+分子 #31: 18S ribosomal RNA
+分子 #87: 7S RNA
+分子 #93: MAGNESIUM ION
+分子 #94: ZINC 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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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 FIELDBright-field microscopy |
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 |
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-6r6g: |