+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-37247 | |||||||||
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タイトル | CULLIN3-KLHL22-RBX1 E3 ligase | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | E3 ligase / STRUCTURAL PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division ...liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / cullin-RING-type E3 NEDD8 transferase / cellular response to chemical stress / RHOBTB3 ATPase cycle / NEDD8 transferase activity / cellular response to L-leucine / cullin-RING ubiquitin ligase complex / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / Notch binding / NEDD8 ligase activity / RHOBTB1 GTPase cycle / Cul5-RING ubiquitin ligase complex / fibroblast apoptotic process / negative regulation of response to oxidative stress / ubiquitin-ubiquitin ligase activity / SCF ubiquitin ligase complex / negative regulation of Rho protein signal transduction / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / mitotic metaphase chromosome alignment / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / intercellular bridge / stress fiber assembly / mitotic spindle assembly checkpoint signaling / Prolactin receptor signaling / positive regulation of cytokinesis / protein monoubiquitination / mitotic sister chromatid segregation / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / sperm flagellum / RHOBTB2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / protein autoubiquitination / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / gastrulation / 14-3-3 protein binding / T cell activation / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / negative regulation of autophagy / intrinsic apoptotic signaling pathway / cyclin binding / Regulation of BACH1 activity / post-translational protein modification / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / cellular response to amino acid stimulus / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RING-type E3 ubiquitin transferase / DNA Damage Recognition in GG-NER / protein destabilization / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / mitotic spindle / Evasion by RSV of host interferon responses / Wnt signaling pathway / NOTCH1 Intracellular Domain Regulates Transcription / spindle pole / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER 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: 3.67 Å | |||||||||
データ登録者 | Su M-Y | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Structure / 年: 2023 タイトル: Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme. 著者: Fei Teng / Yang Wang / Ming Liu / Shuyun Tian / Goran Stjepanovic / Ming-Yuan Su / 要旨: CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric ...CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric BTB-Kelch family proteins combine adapter and substrate receptor into a single polypeptide for the CULLIN3 family. However, the entire structural assembly and molecular details have not been elucidated to date. Here, we present a cryo-EM structure of the CULLIN3 in complex with Kelch-like protein 22 (KLHL22) and a mitochondrial glutamate dehydrogenase complex I (GDH1) at 3.06 Å resolution. The structure adopts a W-shaped architecture formed by E3 ligase dimers. Three CULLIN3 dimers were found to be dynamically associated with a single GDH1 hexamer. CULLIN3 ligase mediated the polyubiquitination of GDH1 in vitro. Together, these results enabled the establishment of a structural model for understanding the complete assembly of BTB-Kelch proteins with CULLIN3 and how together they recognize oligomeric substrates and target them for ubiquitination. | |||||||||
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_37247.map.gz | 208 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-37247-v30.xml emd-37247.xml | 18.4 KB 18.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_37247.png | 28.4 KB | ||
Filedesc metadata | emd-37247.cif.gz | 6.2 KB | ||
その他 | emd_37247_additional_1.map.gz emd_37247_half_map_1.map.gz emd_37247_half_map_2.map.gz | 372 MB 392 MB 392 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-37247 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37247 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_37247_validation.pdf.gz | 778.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_37247_full_validation.pdf.gz | 778.2 KB | 表示 | |
XML形式データ | emd_37247_validation.xml.gz | 18 KB | 表示 | |
CIF形式データ | emd_37247_validation.cif.gz | 21.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37247 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37247 | 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_37247.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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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: 0.85 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: #1
ファイル | emd_37247_additional_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: #2
ファイル | emd_37247_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_37247_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 : CULLIN3-KLHL22-RBX1 E3 ligase
全体 | 名称: CULLIN3-KLHL22-RBX1 E3 ligase |
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要素 |
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-超分子 #1: CULLIN3-KLHL22-RBX1 E3 ligase
超分子 | 名称: CULLIN3-KLHL22-RBX1 E3 ligase / 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 #1: Kelch-like protein 22
分子 | 名称: Kelch-like protein 22 / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 71.744594 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MAEEQEFTQL CKLPAQPSHP HCVNNTYRSA QHSQALLRGL LALRDSGILF DVVLVVEGRH IEAHRILLAA SCDYFRGMFA GGLKEMEQE EVLIHGVSYN AMCQILHFIY TSELELSLSN VQETLVAACQ LQIPEIIHFC CDFLMSWVDE ENILDVYRLA E LFDLSRLT ...文字列: MAEEQEFTQL CKLPAQPSHP HCVNNTYRSA QHSQALLRGL LALRDSGILF DVVLVVEGRH IEAHRILLAA SCDYFRGMFA GGLKEMEQE EVLIHGVSYN AMCQILHFIY TSELELSLSN VQETLVAACQ LQIPEIIHFC CDFLMSWVDE ENILDVYRLA E LFDLSRLT EQLDTYILKN FVAFSRTDKY RQLPLEKVYS LLSSNRLEVS CETEVYEGAL LYHYSLEQVQ ADQISLHEPP KL LETVRFP LMEAEVLQRL HDKLDPSPLR DTVASALMYH RNESLQPSLQ SPQTELRSDF QCVVGFGGIH STPSTVLSDQ AKY LNPLLG EWKHFTASLA PRMSNQGIAV LNNFVYLIGG DNNVQGFRAE SRCWRYDPRH NRWFQIQSLQ QEHADLSVCV VGRY IYAVA GRDYHNDLNA VERYDPATNS WAYVAPLKRE VYAHAGATLE GKMYITCGRR GEDYLKETHC YDPGSNTWHT LADGP VRRA WHGMATLLNK LYVIGGSNND AGYRRDVHQV ACYSCTSGQW SSVCPLPAGH GEPGIAVLDN RIYVLGGRSH NRGSRT GYV HIYDVEKDCW EEGPQLDNSI SGLAACVLTL PRSLLLEPPR GTPDRSQADP DFASEVMSVS DWEEFDNSSE D UniProtKB: Kelch-like protein 22 |
-分子 #2: Cullin-3
分子 | 名称: Cullin-3 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 89.063328 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM ...文字列: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKV REDVLNSLNN NFLQTLNQAW NDHQTAMVMI RDILMYMDRV YVQQNNVENV YNLGLIIFRD QVVRYGCIRD H LRQTLLDM IARERKGEVV DRGAIRNACQ MLMILGLEGR SVYEEDFEAP FLEMSAEFFQ MESQKFLAEN SASVYIKKVE AR INEEIER VMHCLDKSTE EPIVKVVERE LISKHMKTIV EMENSGLVHM LKNGKTEDLG CMYKLFSRVP NGLKTMCECM SSY LREQGK ALVSEEGEGK NPVDYIQGLL DLKSRFDRFL LESFNNDRLF KQTIAGDFEY FLNLNSRSPE YLSLFIDDKL KKGV KGLTE QEVETILDKA MVLFRFMQEK DVFERYYKQH LARRLLTNKS VSDDSEKNMI SKLKTECGCQ FTSKLEGMFR DMSIS NTTM DEFRQHLQAT GVSLGGVDLT VRVLTTGYWP TQSATPKCNI PPAPRHAFEI FRRFYLAKHS GRQLTLQHHM GSADLN ATF YGPVKKEDGS EVGVGGAQVT GSNTRKHILQ VSTFQMTILM LFNNREKYTF EEIQQETDIP ERELVRALQS LACGKPT QR VLTKEPKSKE IENGHIFTVN DQFTSKLHRV KIQTVAAKQG ESDPERKETR QKVDDDRKHE IEAAIVRIMK SRKKMQHN V LVAEVTQQLK ARFLPSPVVI KKRIEGLIER EYLARTPEDR KVYTYVA UniProtKB: Cullin-3 |
-分子 #3: E3 ubiquitin-protein ligase RBX1
分子 | 名称: E3 ubiquitin-protein ligase RBX1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO / EC番号: RING-type E3 ubiquitin transferase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 12.289977 KDa |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH UniProtKB: E3 ubiquitin-protein ligase RBX1 |
-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: 7.4 |
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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: GATAN K3 (6k x 4k) / 平均電子線量: 1.07 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 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): 1.1 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: INSILICO MODEL |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.67 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 181834 |
初期 角度割当 | タイプ: OTHER |
最終 角度割当 | タイプ: OTHER |