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データを開く
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基本情報
| 登録情報 | ![]() | |||||||||
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| タイトル | Structure of a GRP94 folding intermediate engaged with a CCDC134- and FKBP11-bound secretory translocon | |||||||||
マップデータ | Whole particle (RTC) map after focused refinement on the 60S subunit | |||||||||
試料 |
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キーワード | Ribosome / Membrane protein / Translocon / Transport / N-Glycosylation | |||||||||
| 機能・相同性 | 機能・相同性情報positive regulation of MyD88-dependent toll-like receptor signaling pathway / positive regulation of toll-like receptor signaling pathway / oligosaccharyltransferase complex binding / actin rod assembly / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / muscle organ morphogenesis / Asparagine N-linked glycosylation / embryonic liver development / regulation of glycoprotein biosynthetic process ...positive regulation of MyD88-dependent toll-like receptor signaling pathway / positive regulation of toll-like receptor signaling pathway / oligosaccharyltransferase complex binding / actin rod assembly / oligosaccharyltransferase complex A / oligosaccharyltransferase complex B / muscle organ morphogenesis / Asparagine N-linked glycosylation / embryonic liver development / regulation of glycoprotein biosynthetic process / ATF6 (ATF6-alpha) activates chaperone genes / endoplasmic reticulum Sec complex / pronephric nephron development / endoplasmic reticulum chaperone complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / : / cotranslational protein targeting to membrane / endoplasmic reticulum quality control compartment / Ssh1 translocon complex / plasma membrane organization / Sec61 translocon complex / positive regulation of growth hormone secretion / protein folding in endoplasmic reticulum / sarcoplasmic reticulum lumen / protein insertion into ER membrane / oligosaccharyltransferase complex / post-translational protein targeting to endoplasmic reticulum membrane / protein targeting to ER / positive regulation of organ growth / ventricular system development / : / SRP-dependent cotranslational protein targeting to membrane, translocation / XBP1(S) activates chaperone genes / glycoprotein biosynthetic process / SRP-dependent cotranslational protein targeting to membrane / signal sequence binding / translation at presynapse / protein N-linked glycosylation / post-translational protein targeting to membrane, translocation / endoplasmic reticulum organization / exit from mitosis / optic nerve development / response to insecticide / Trafficking and processing of endosomal TLR / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / epithelial cell apoptotic process / negative regulation of formation of translation preinitiation complex / axial mesoderm development / ribosomal protein import into nucleus / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 90S preribosome assembly / embryonic hemopoiesis / alpha-beta T cell differentiation / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / insulin secretion / Scavenging by Class A Receptors / epidermal growth factor binding / TORC2 complex binding / azurophil granule membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / retrograde protein transport, ER to cytosol / low-density lipoprotein particle receptor binding / G1 to G0 transition / protein phosphatase inhibitor activity / middle ear morphogenesis / Regulation of CDH1 posttranslational processing and trafficking to plasma membrane / sperm plasma membrane / cytoplasmic side of rough endoplasmic reticulum membrane / cellular response to ATP / homeostatic process / smooth endoplasmic reticulum / macrophage chemotaxis / lung morphogenesis / positive regulation of natural killer cell proliferation / male meiosis I / Protein hydroxylation / Advanced glycosylation endproduct receptor signaling / intracellular membrane-bounded organelle / Peptide chain elongation / regulation of ossification / protein secretion / transmembrane protein transporter activity / Selenocysteine synthesis / Formation of a pool of free 40S subunits / blastocyst development / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / ubiquitin ligase inhibitor activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / response to type II interferon / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit 類似検索 - 分子機能 | |||||||||
| 生物種 | Homo sapiens (ヒト) | |||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | |||||||||
データ登録者 | Yamsek M / Jha R / Keenan RJ | |||||||||
| 資金援助 | 米国, 1件
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引用 | ジャーナル: Science / 年: 2024 タイトル: Regulated N-glycosylation controls chaperone function and receptor trafficking. 著者: Mengxiao Ma / Ramin Dubey / Annie Jen / Ganesh V Pusapati / Bharti Singal / Evgenia Shishkova / Katherine A Overmyer / Valérie Cormier-Daire / Juliette Fedry / L Aravind / Joshua J Coon / Rajat Rohatgi / ![]() 要旨: One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a ...One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCDC134, an ER luminal protein. During its translocation into the ER, an N-terminal peptide in HSP90B1 templates the assembly of a translocon complex containing CCDC134 and OST-A that protects HSP90B1 during folding, preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT and IGF1R signaling and causes the bone developmental disorder osteogenesis imperfecta. Thus, N-glycosylation can be regulated by specificity factors in the ER to control cell surface receptor signaling and tissue development. | |||||||||
| 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_49171.map.gz | 340.4 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-49171-v30.xml emd-49171.xml | 102.9 KB 102.9 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_49171_fsc.xml | 16.9 KB | 表示 | FSCデータファイル |
| 画像 | emd_49171.png | 121.2 KB | ||
| マスクデータ | emd_49171_msk_1.map | 421.9 MB | マスクマップ | |
| Filedesc metadata | emd-49171.cif.gz | 21.7 KB | ||
| その他 | emd_49171_half_map_1.map.gz emd_49171_half_map_2.map.gz | 341.1 MB 341.1 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-49171 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-49171 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9n9jMC ![]() 9ygyC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_49171.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 注釈 | Whole particle (RTC) map after focused refinement on the 60S subunit | ||||||||||||||||||||||||||||||||||||
| 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: 1.40243 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
-マスク #1
| ファイル | emd_49171_msk_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: Half-map 1
| ファイル | emd_49171_half_map_1.map | ||||||||||||
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| 注釈 | Half-map 1 | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: Half-map 2
| ファイル | emd_49171_half_map_2.map | ||||||||||||
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| 注釈 | Half-map 2 | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
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試料の構成要素
+全体 : Nascent GRP94 folding intermediate bound to a ribosome-translocon...
+超分子 #1: Nascent GRP94 folding intermediate bound to a ribosome-translocon...
+分子 #1: Translocon-associated protein subunit alpha
+分子 #2: Translocon-associated protein subunit beta
+分子 #3: Translocon-associated protein subunit gamma
+分子 #4: Translocon-associated protein subunit delta
+分子 #5: Peptidyl-prolyl cis-trans isomerase FKBP11
+分子 #6: Coiled-coil domain-containing protein 134
+分子 #7: Protein transport protein Sec61 subunit alpha isoform 1
+分子 #8: Protein transport protein Sec61 subunit beta
+分子 #9: Protein transport protein Sec61 subunit gamma
+分子 #10: Stress-associated endoplasmic reticulum protein 1
+分子 #11: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #12: Oligosaccharyltransferase complex subunit OSTC
+分子 #13: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #14: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #18: 60S ribosomal protein L8
+分子 #19: 60S ribosomal protein L3
+分子 #20: Large ribosomal subunit protein uL4
+分子 #21: Large ribosomal subunit protein uL18
+分子 #22: Large ribosomal subunit protein eL6
+分子 #23: 60S ribosomal protein L7
+分子 #24: Large ribosomal subunit protein eL8
+分子 #25: Large ribosomal subunit protein uL6
+分子 #26: Ribosomal protein uL16-like
+分子 #27: Large ribosomal subunit protein eL13
+分子 #28: Large ribosomal subunit protein eL14
+分子 #29: Large ribosomal subunit protein eL15
+分子 #30: Large ribosomal subunit protein uL13
+分子 #31: Large ribosomal subunit protein uL22
+分子 #32: Large ribosomal subunit protein eL18
+分子 #33: Large ribosomal subunit protein eL19
+分子 #34: Large ribosomal subunit protein eL20
+分子 #35: Large ribosomal subunit protein eL21
+分子 #36: Large ribosomal subunit protein eL22
+分子 #37: Large ribosomal subunit protein uL14
+分子 #38: Large ribosomal subunit protein eL24
+分子 #39: Large ribosomal subunit protein uL23
+分子 #40: Large ribosomal subunit protein uL24
+分子 #41: Large ribosomal subunit protein eL27
+分子 #42: 60S ribosomal protein L27a
+分子 #43: 60S ribosomal protein L29
+分子 #44: Large ribosomal subunit protein eL30
+分子 #45: Large ribosomal subunit protein eL31
+分子 #46: Large ribosomal subunit protein eL32
+分子 #47: Large ribosomal subunit protein eL33
+分子 #48: Large ribosomal subunit protein eL34
+分子 #49: Large ribosomal subunit protein uL29
+分子 #50: Large ribosomal subunit protein eL36
+分子 #51: Large ribosomal subunit protein eL37
+分子 #52: Large ribosomal subunit protein eL38
+分子 #53: Large ribosomal subunit protein eL39
+分子 #54: Ubiquitin-60S ribosomal protein L40
+分子 #55: Small ribosomal subunit protein eS32
+分子 #56: Large ribosomal subunit protein eL42
+分子 #57: Large ribosomal subunit protein eL43
+分子 #58: 60S ribosomal protein L28
+分子 #59: 60S acidic ribosomal protein P0
+分子 #60: 60S ribosomal protein L12
+分子 #61: 60S ribosomal protein L10a
+分子 #62: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #63: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #64: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...
+分子 #65: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #66: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+分子 #69: Endoplasmin
+分子 #70: Large ribosomal subunit protein uL5
+分子 #15: 28S ribosomal RNA
+分子 #16: 5S ribosomal RNA
+分子 #17: 5.8S ribosomal RNA
+分子 #67: tRNA
+分子 #68: tRNA
+分子 #75: phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,1...
+分子 #76: MAGNESIUM ION
+分子 #77: ZINC ION
+分子 #78: water
-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 |
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試料調製
| 濃度 | 0.056 mg/mL | |||||||||||||||||||||
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| 緩衝液 | pH: 7.4 構成要素:
詳細: HEPES buffer was adjusted to pH 7.4 with potassium hydroxide. | |||||||||||||||||||||
| グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 25 sec. | |||||||||||||||||||||
| 凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 295 K / 装置: FEI VITROBOT MARK IV 詳細: Three microliters of affinity-purified RTCs were applied to the grid, incubated for 60 seconds, blotted for 7 seconds, drained for 0.5 seconds, and frozen in liquid nitrogen-cooled ethane.. | |||||||||||||||||||||
| 詳細 | Native ribosome-translocon complexes isolated from HEK293 microsomes by affinity purification via a Flag-tag on FKBP11 |
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電子顕微鏡法
| 顕微鏡 | TFS KRIOS |
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| 撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 6569 / 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm 最大 デフォーカス(公称値): 1.9000000000000001 µm 最小 デフォーカス(公称値): 0.9 µm / 倍率(公称値): 53000 |
| 試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
| 詳細 | Tightly restrained real-space refinement in Coot and Phenix |
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| 精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
| 得られたモデル | ![]() PDB-9n9j: |
ムービー
コントローラー
万見について




キーワード
Homo sapiens (ヒト)
データ登録者
米国, 1件
引用














































Z (Sec.)
Y (Row.)
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FIELD EMISSION GUN

