+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-33768 | |||||||||
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タイトル | Human O-GlcNAc transferase Dimer | |||||||||
マップデータ | Human OGT Dimer | |||||||||
試料 |
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キーワード | Human O-GlcNAc transferase Dimer / TRANSFERASE | |||||||||
機能・相同性 | 機能・相同性情報 protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of proteolysis / hemopoiesis / mitophagy / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / cell projection / positive regulation of translation / mitochondrial membrane / cellular response to glucose stimulus / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Regulation of necroptotic cell death / protein processing / chromatin DNA binding / UCH proteinases / chromatin organization / positive regulation of cold-induced thermogenesis / HATs acetylate histones / glutamatergic synapse / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol 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: 3.82 Å | |||||||||
データ登録者 | Gao H / Lu P / Liu Y | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Cryo-EM structure of human O-GlcNAcylation enzyme pair OGT-OGA complex. 著者: Ping Lu / Yusong Liu / Maozhou He / Ting Cao / Mengquan Yang / Shutao Qi / Hongtao Yu / Haishan Gao / 要旨: O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O- ...O-GlcNAcylation is a conserved post-translational modification that attaches N-acetyl glucosamine (GlcNAc) to myriad cellular proteins. In response to nutritional and hormonal signals, O-GlcNAcylation regulates diverse cellular processes by modulating the stability, structure, and function of target proteins. Dysregulation of O-GlcNAcylation has been implicated in the pathogenesis of cancer, diabetes, and neurodegeneration. A single pair of enzymes, the O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), catalyzes the addition and removal of O-GlcNAc on over 3,000 proteins in the human proteome. However, how OGT selects its native substrates and maintains the homeostatic control of O-GlcNAcylation of so many substrates against OGA is not fully understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of human OGT and the OGT-OGA complex. Our studies reveal that OGT forms a functionally important scissor-shaped dimer. Within the OGT-OGA complex structure, a long flexible OGA segment occupies the extended substrate-binding groove of OGT and positions a serine for O-GlcNAcylation, thus preventing OGT from modifying other substrates. Conversely, OGT disrupts the functional dimerization of OGA and occludes its active site, resulting in the blocking of access by other substrates. This mutual inhibition between OGT and OGA may limit the futile O-GlcNAcylation cycles and help to maintain O-GlcNAc homeostasis. | |||||||||
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_33768.map.gz | 229.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-33768-v30.xml emd-33768.xml | 17.9 KB 17.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_33768.png | 103.4 KB | ||
Filedesc metadata | emd-33768.cif.gz | 6.3 KB | ||
その他 | emd_33768_half_map_1.map.gz emd_33768_half_map_2.map.gz | 226.1 MB 226 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-33768 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33768 | 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_33768.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Human OGT Dimer | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.861 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
-ハーフマップ: Half map
ファイル | emd_33768_half_map_1.map | ||||||||||||
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注釈 | Half map | ||||||||||||
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
ファイル | emd_33768_half_map_2.map | ||||||||||||
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注釈 | Half map | ||||||||||||
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 : Human O-GlcNAc transferase (OGT)
全体 | 名称: Human O-GlcNAc transferase (OGT) |
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要素 |
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-超分子 #1: Human O-GlcNAc transferase (OGT)
超分子 | 名称: Human O-GlcNAc transferase (OGT) / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 250 KDa |
-分子 #1: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase ...
分子 | 名称: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: protein O-GlcNAc transferase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 117.937367 KDa |
組換発現 | 生物種: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) |
配列 | 文字列: MASSVGNVAD STEPTKRMLS FQGPMELAHR EYQAGDFEAA ERHCMQLWRQ EPDNTGVLLL LSSIHFECRR LDRSAHFSTL AIKQNPLLA EAYSNLGNVY KERGQLQEAI EHYRHALRLK PDFIDGYINL AAALVAAGDM EGAVQAYVSA LQYNPDLYCV R SDLGNLLK ...文字列: MASSVGNVAD STEPTKRMLS FQGPMELAHR EYQAGDFEAA ERHCMQLWRQ EPDNTGVLLL LSSIHFECRR LDRSAHFSTL AIKQNPLLA EAYSNLGNVY KERGQLQEAI EHYRHALRLK PDFIDGYINL AAALVAAGDM EGAVQAYVSA LQYNPDLYCV R SDLGNLLK ALGRLEEAKA CYLKAIETQP NFAVAWSNLG CVFNAQGEIW LAIHHFEKAV TLDPNFLDAY INLGNVLKEA RI FDRAVAA YLRALSLSPN HAVVHGNLAC VYYEQGLIDL AIDTYRRAIE LQPHFPDAYC NLANALKEKG SVAEAEDCYN TAL RLCPTH ADSLNNLANI KREQGNIEEA VRLYRKALEV FPEFAAAHSN LASVLQQQGK LQEALMHYKE AIRISPTFAD AYSN MGNTL KEMQDVQGAL QCYTRAIQIN PAFADAHSNL ASIHKDSGNI PEAIASYRTA LKLKPDFPDA YCNLAHCLQI VCDWT DYDE RMKKLVSIVA DQLEKNRLPS VHPHHSMLYP LSHGFRKAIA ERHGNLCLDK INVLHKPPYE HPKDLKLSDG RLRVGY VSS DFGNHPTSHL MQSIPGMHNP DKFEVFCYAL SPDDGTNFRV KVMAEANHFI DLSQIPCNGK AADRIHQDGI HILVNMN GY TKGARNELFA LRPAPIQAMW LGYPGTSGAL FMDYIITDQE TSPAEVAEQY SEKLAYMPHT FFIGDHANMF PHLKKKAV I DFKSNGHIYD NRIVLNGIDL KAFLDSLPDV KIVKMKCPDG GDNADSSNTA LNMPVIPMNT IAEAVIEMIN RGQIQITIN GFSISNGLAT TQINNKAATG EEVPRTIIVT TRSQYGLPED AIVYCNFNQL YKIDPSTLQM WANILKRVPN SVLWLLRFPA VGEPNIQQY AQNMGLPQNR IIFSPVAPKE EHVRRGQLAD VCLDTPLCNG HTTGMDVLWA GTPMVTMPGE TLASRVAASQ L TCLGCLEL IAKNRQEYED IAVKLGTDLE YLKKVRGKVW KQRISSPLFN TKQYTMELER LYLQMWEHYA AGNKPDHMIK PV EVTESAH HHHHH UniProtKB: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit |
-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
濃度 | 5 mg/mL |
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緩衝液 | pH: 7.5 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 5539 / 平均露光時間: 0.0725 sec. / 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 100.0 µm / 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): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 105000 |
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 |