+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16232 | |||||||||
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タイトル | Structure of the TRAP complex with the Sec translocon and a translating ribosome | |||||||||
マップデータ | high-resolution map | |||||||||
試料 |
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キーワード | ER targeting / protein translocation / ER protein biogenesis / TRANSLOCASE | |||||||||
機能・相同性 | 機能・相同性情報 Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / endoplasmic reticulum Sec complex / pronephric nephron development / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / endoplasmic reticulum Sec complex / pronephric nephron development / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / signal sequence binding / post-translational protein targeting to membrane, translocation / negative regulation of RNA splicing / regulation of G1 to G0 transition / laminin receptor activity / 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 / 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 / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / guanyl-nucleotide exchange factor activity / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / phospholipid binding / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / virus receptor activity / ribosome biogenesis / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / canis lupus familiaris (イヌ) / 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: 3.5 Å | |||||||||
データ登録者 | Jaskolowski M / Jomaa A / Gamerdinger M / Shrestha S / Leibundgut M / Deuerling E / Ban N | |||||||||
資金援助 | スイス, 2件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2023 タイトル: Molecular basis of the TRAP complex function in ER protein biogenesis. 著者: Mateusz Jaskolowski / Ahmad Jomaa / Martin Gamerdinger / Sandeep Shrestha / Marc Leibundgut / Elke Deuerling / Nenad Ban / 要旨: The translocon-associated protein (TRAP) complex resides in the endoplasmic reticulum (ER) membrane and interacts with the Sec translocon and the ribosome to facilitate biogenesis of secretory and ...The translocon-associated protein (TRAP) complex resides in the endoplasmic reticulum (ER) membrane and interacts with the Sec translocon and the ribosome to facilitate biogenesis of secretory and membrane proteins. TRAP plays a key role in the secretion of many hormones, including insulin. Here we reveal the molecular architecture of the mammalian TRAP complex and how it engages the translating ribosome associated with Sec61 translocon on the ER membrane. The TRAP complex is anchored to the ribosome via a long tether and its position is further stabilized by a finger-like loop. This positions a cradle-like lumenal domain of TRAP below the translocon for interactions with translocated nascent chains. Our structure-guided TRAP mutations in Caenorhabditis elegans lead to growth deficits associated with increased ER stress and defects in protein hormone secretion. These findings elucidate the molecular basis of the TRAP complex in the biogenesis and translocation of proteins at the ER. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_16232.map.gz | 475.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16232-v30.xml emd-16232.xml | 132.7 KB 132.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16232_fsc.xml | 18.1 KB | 表示 | FSCデータファイル |
画像 | emd_16232.png | 193.7 KB | ||
Filedesc metadata | emd-16232.cif.gz | 24.3 KB | ||
その他 | emd_16232_additional_1.map.gz emd_16232_half_map_1.map.gz emd_16232_half_map_2.map.gz | 474 MB 414.5 MB 414.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16232 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16232 | HTTPS FTP |
-関連構造データ
関連構造データ | 8btkMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_16232.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | high-resolution map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: map filtered to 5A resolution
ファイル | emd_16232_additional_1.map | ||||||||||||
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注釈 | map filtered to 5A resolution | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_16232_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_16232_half_map_2.map | ||||||||||||
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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 the TRAP complex with the Sec translocon and a trans...
+超分子 #1: Structure of the TRAP complex with the Sec translocon and a trans...
+超分子 #2: Ribosomal large subunit (60S)
+超分子 #3: Ribosomal small subunit (SSU)
+超分子 #4: P-site tRNA
+超分子 #5: Sec61 translocon
+超分子 #6: TRAP complex
+分子 #1: 28S rRNA
+分子 #2: 5S rRNA
+分子 #3: 5.8S rRNA
+分子 #52: 18S rRNA
+分子 #60: mRNA
+分子 #61: P-site tRNA
+分子 #4: 60S ribosomal protein L8
+分子 #5: Ribosomal protein L3
+分子 #6: 60S ribosomal protein L4
+分子 #7: Ribosomal_L18_c domain-containing protein
+分子 #8: 60S ribosomal protein L6
+分子 #9: uL30,60S ribosomal protein L7
+分子 #10: 60S ribosomal protein L7a
+分子 #11: 60S ribosomal protein L9
+分子 #12: Ribosomal protein L10
+分子 #13: Ribosomal protein L11
+分子 #14: Nascent chain
+分子 #15: L13
+分子 #16: Ribosomal protein L14
+分子 #17: Ribosomal protein L15
+分子 #18: 60S ribosomal protein L13a
+分子 #19: uL22
+分子 #20: eL18
+分子 #21: 60S ribosomal protein L19
+分子 #22: 60S ribosomal protein L18a
+分子 #23: 60S ribosomal protein L21
+分子 #24: 60S ribosomal protein L22
+分子 #25: Ribosomal protein L23
+分子 #26: Ribosomal protein L24
+分子 #27: Ribosomal_L23eN domain-containing protein
+分子 #28: Ribosomal protein L26
+分子 #29: 60S ribosomal protein L27
+分子 #30: 60S ribosomal protein L27a
+分子 #31: 60S ribosomal protein L29
+分子 #32: eL30
+分子 #33: Ribosomal protein L31
+分子 #34: eL32
+分子 #35: 60S ribosomal protein L35a
+分子 #36: 60S ribosomal protein L34
+分子 #37: 60S ribosomal protein L35
+分子 #38: 60S ribosomal protein L36
+分子 #39: Ribosomal protein L37
+分子 #40: eL38
+分子 #41: eL39
+分子 #42: Ubiquitin
+分子 #43: eL42
+分子 #44: eL43
+分子 #45: 60S ribosomal protein L28
+分子 #46: 60S acidic ribosomal protein P0
+分子 #47: Ribosomal protein L12
+分子 #48: Ribosomal protein uL1
+分子 #49: Protein transport protein Sec61 subunit alpha isoform 1
+分子 #50: Protein transport protein Sec61 subunit gamma
+分子 #51: Protein transport protein Sec61 subunit beta
+分子 #53: 40S ribosomal protein S27
+分子 #54: Ribosomal protein S28
+分子 #55: Ribosomal protein S27a
+分子 #56: 40S ribosomal protein S30
+分子 #57: eS26
+分子 #58: RACK1
+分子 #59: uS14
+分子 #62: 40S ribosomal protein SA
+分子 #63: 40S ribosomal protein S3a
+分子 #64: Ribosomal_S5_C domain-containing protein,40S ribosomal protein S2
+分子 #65: 40S ribosomal protein S3
+分子 #66: 40S ribosomal protein S4
+分子 #67: Ribosomal protein S5
+分子 #68: 40S ribosomal protein S6
+分子 #69: 40S ribosomal protein S7
+分子 #70: 40S ribosomal protein S8
+分子 #71: Ribosomal protein S9 (Predicted)
+分子 #72: Ribosomal protein eS10
+分子 #73: 40S ribosomal protein S11
+分子 #74: 40S ribosomal protein S12
+分子 #75: uS15
+分子 #76: 40S ribosomal protein S14
+分子 #77: 40S ribosomal protein uS19
+分子 #78: uS9
+分子 #79: 40S ribosomal protein eS17
+分子 #80: 40S ribosomal protein S18
+分子 #81: 40S ribosomal protein S19
+分子 #82: 40S ribosomal protein uS10
+分子 #83: 40S ribosomal protein S21
+分子 #84: Ribosomal protein S15a
+分子 #85: 40S ribosomal protein S23
+分子 #86: 40S ribosomal protein S24
+分子 #87: 40S ribosomal protein S25
+分子 #88: 60S ribosomal protein L41
+分子 #89: Translocon-associated protein subunit alpha
+分子 #90: Translocon-associated protein subunit beta
+分子 #91: Signal sequence receptor subunit 3
+分子 #92: Translocon-associated protein subunit delta
+分子 #93: SPERMIDINE
+分子 #94: SPERMINE
+分子 #95: MAGNESIUM ION
+分子 #96: GUANOSINE-5'-TRIPHOSPHATE
+分子 #97: ACETYLAMINO-ACETIC ACID
+分子 #98: 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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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 15 sec. / 詳細: 15 mA for 15 seconds in Pelco EasyGlow system |
凍結 | 凍結剤: ETHANE-PROPANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV 詳細: 3.5 uL of sample was incubated on the grid for 60 seconds at 4*C and 100% humidity before being blotted and plunged into liquid ethane/propane mix cooled to liquid nitrogen temperature. |
-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: GATAN K3 (6k x 4k) / 平均電子線量: 60.0 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: OTHER / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.2 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |