+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-41997 | |||||||||
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タイトル | KCTD5/Cullin3/Gbeta1gamma2 Complex State A: Reference Map for Composite Map EMD-41996 | |||||||||
マップデータ | KCTD5_cul3_Gbg Relion 3Drefine reference full map | |||||||||
試料 |
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キーワード | cullin family protein / proteasome-mediated ubiquitin-dependent protein catabolic process / complex / ubiquitin-dependent protein catabolic process / CYTOSOLIC 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 / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / ubiquitin ligase complex scaffold activity / negative regulation of type I interferon production / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / protein monoubiquitination / positive regulation of cytokinesis / cyclin binding / sperm flagellum / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / protein autoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / regulation of cellular response to insulin stimulus / gastrulation / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / cellular response to amino acid stimulus / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / Hedgehog 'on' state / protein destabilization / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / G1/S transition of mitotic cell cycle / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / mitotic spindle / Wnt signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / spindle pole / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / Regulation of RAS by GAPs / protein polyubiquitination / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / ubiquitin protein ligase activity / KEAP1-NFE2L2 pathway / G alpha (12/13) signalling events / extracellular vesicle / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor complex adaptor activity / cell migration / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / Neddylation / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / G alpha (i) signalling events / fibroblast proliferation / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / Potential therapeutics for SARS 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: 3.96 Å | |||||||||
データ登録者 | Nguyen DM / Narayanan N / Kuntz DA / Prive GG | |||||||||
資金援助 | カナダ, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2024 タイトル: Structure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex. 著者: Duc Minh Nguyen / Deanna H Rath / Dominic Devost / Darlaine Pétrin / Robert Rizk / Alan X Ji / Naveen Narayanan / Darren Yong / Andrew Zhai / Douglas A Kuntz / Maha U Q Mian / Neil C Pomroy ...著者: Duc Minh Nguyen / Deanna H Rath / Dominic Devost / Darlaine Pétrin / Robert Rizk / Alan X Ji / Naveen Narayanan / Darren Yong / Andrew Zhai / Douglas A Kuntz / Maha U Q Mian / Neil C Pomroy / Alexander F A Keszei / Samir Benlekbir / Mohammad T Mazhab-Jafari / John L Rubinstein / Terence E Hébert / Gilbert G Privé / 要旨: Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C- ...Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain, engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3/Gβγ assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5/CUL3 and KCTD5/Gβγ moieties of the structure. CRL3 engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 superassembly, and extension of the structure to include full-length CUL3 with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3/Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex. #1: ジャーナル: Biorxiv / 年: 2023 タイトル: Structure and dynamics of a pentameric KCTD5/Cullin3/G beta gamma E3 ubiquitin ligase complex 著者: Nguyen DM / Rath DH / Devost D / Petrin D / Rizk R / Ji AX / Narayanan N / Yong D / Zhai A / Kuntz DA / Mian MUQ / Pomroy NC / Keszei AFE / Benlekbir S / Mazhab-Jafari MT / Rubinstein JL / Hebert TE / Prive GG | |||||||||
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_41997.map.gz | 102 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-41997-v30.xml emd-41997.xml | 20.1 KB 20.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_41997_fsc.xml | 11.6 KB | 表示 | FSCデータファイル |
画像 | emd_41997.png | 107.5 KB | ||
マスクデータ | emd_41997_msk_1.map | 129.7 MB | マスクマップ | |
Filedesc metadata | emd-41997.cif.gz | 6.1 KB | ||
その他 | emd_41997_half_map_1.map.gz emd_41997_half_map_2.map.gz | 102.4 MB 102.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-41997 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41997 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_41997_validation.pdf.gz | 833 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_41997_full_validation.pdf.gz | 832.5 KB | 表示 | |
XML形式データ | emd_41997_validation.xml.gz | 18.5 KB | 表示 | |
CIF形式データ | emd_41997_validation.cif.gz | 23.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41997 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41997 | 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_41997.map.gz / 形式: CCP4 / 大きさ: 129.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | KCTD5_cul3_Gbg Relion 3Drefine reference full map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.03 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_41997_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: KCTD5 cul3 Gbg Relion 3Drefine reference half map 2
ファイル | emd_41997_half_map_1.map | ||||||||||||
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注釈 | KCTD5_cul3_Gbg Relion 3Drefine reference half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: KCTD5 cul3 Gbg Relion 3Drefine reference half map 1
ファイル | emd_41997_half_map_2.map | ||||||||||||
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注釈 | KCTD5_cul3_Gbg Relion 3Drefine reference half map 1 | ||||||||||||
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 : Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...
全体 | 名称: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma |
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要素 |
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-超分子 #1: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gb...
超分子 | 名称: Complex of substrate adaptor KCTD5 with Cullin-3 and substrate Gbeta-gamma 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: KCTD5
分子 | 名称: KCTD5 / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MAENHCELLS PARGGIGAGL GGGLCRRCSA GLGALAQRPG SVSKWVRLNV GGTYFLTTRQ TLCRDPKSF LYRLCQADPD LDSDKDETGA YLIDRDPTYF GPVLNYLRHG KLVINKDLAE E GVLEEAEF YNITSLIKLV KDKIRERDSK TSQVPVKHVY RVLQCQEEEL ...文字列: MAENHCELLS PARGGIGAGL GGGLCRRCSA GLGALAQRPG SVSKWVRLNV GGTYFLTTRQ TLCRDPKSF LYRLCQADPD LDSDKDETGA YLIDRDPTYF GPVLNYLRHG KLVINKDLAE E GVLEEAEF YNITSLIKLV KDKIRERDSK TSQVPVKHVY RVLQCQEEEL TQMVSTMSDG WK FEQLVSI GSSYNYGNED QAEFLCVVSK ELHNTPYGTA SEPSEKAKIL QERGSRM UniProtKB: UNIPROTKB: Q9XV2 |
-分子 #2: Cullin3 1-381
分子 | 名称: Cullin3 1-381 / タイプ: protein_or_peptide / ID: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKVR EDVLNSLNNN FLQTLNQAWN DHQTAMVMIR DILMYMDRVY VQQNNVENVY NLGLIIFRDQ VVRYGCIRDH LRQTLLDMIA ...文字列: MSNLSKGTGS RKDTKMRIRA FPMTMDEKYV NSIWDLLKNA IQEIQRKNNS GLSFEELYRN AYTMVLHKHG EKLYTGLREV VTEHLINKVR EDVLNSLNNN FLQTLNQAWN DHQTAMVMIR DILMYMDRVY VQQNNVENVY NLGLIIFRDQ VVRYGCIRDH LRQTLLDMIA RERKGEVVDR GAIRNACQML MILGLEGRSV YEEDFEAPFL EMSAEFFQME SQKFLAENSA SVYIKKVEAR INEEIERVMH CLDKSTEEPI VKVVERELIS KHMKTIVEME NSGLVHMLKN GKTEDLGCMY KLFSRVPNGL KTMCECMSSY LREQGKALVS EEGEGKNPVD YIQGLLDLKS RFDRFLLESF NNDRLFKQTI AGDFEYFLNL N UniProtKB: Cullin-3 |
-分子 #3: GBB1_HUMAN
分子 | 名称: GBB1_HUMAN / タイプ: protein_or_peptide / ID: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRL LVSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN I CSIYNLKT REGNVRVSRE LAGHTGYLSC CRFLDDNQIV TSSGDTTCAL ...文字列: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRL LVSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN I CSIYNLKT REGNVRVSRE LAGHTGYLSC CRFLDDNQIV TSSGDTTCAL WDIETGQQTT TF TGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DINAICFFPN GNA FATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDAL KADRA GVLAGHDNRV SCLGVTDDGM AVATGSWDSF LKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-分子 #4: GBG2_HUMAN
分子 | 名称: GBG2_HUMAN / タイプ: protein_or_peptide / ID: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSA IL UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-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 / 装置: FEI VITROBOT MARK IV |
-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: FEI FALCON IV (4k x 4k) 実像数: 7464 / 平均電子線量: 49.35 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 / 最大 デフォーカス(公称値): 1.5 µm / 最小 デフォーカス(公称値): 0.25 µm / 倍率(公称値): 75000 |
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 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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