SASDBR3: Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant): conjugat...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDBR3

試料

Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant): conjugated to Ubiquitin

• E3 ubiquitin-protein ligase RNF8 (protein), RNF8, Homo sapiens
• Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) (protein), Ubc13 - C87K, K92A, Homo sapiens
• Polyubiquitin-C (protein), UBC, Homo sapiens

機能・相同性

分子機能:

UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / sperm DNA condensation / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / protein K6-linked ubiquitination / isotype switching / postreplication repair / positive regulation of intracellular signal transduction / positive regulation of double-strand break repair / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / signal transduction in response to DNA damage / positive regulation of double-strand break repair via homologous recombination / protein autoubiquitination / protein K48-linked ubiquitination / interstrand cross-link repair / regulation of DNA repair / ubiquitin ligase complex / antiviral innate immune response / Maturation of protein E / Maturation of protein E / negative regulation of TORC1 signaling / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / positive regulation of DNA repair / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / epigenetic regulation of gene expression / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling

ドメイン・相同性:

E3 ubiquitin-protein ligase RNF8 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily

構成要素:

E3 ubiquitin-protein ligase RNF8 / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 N

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: J Biol Chem / 年: 2016; タイトル: RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.; 著者: Curtis D Hodge / Ismail H Ismail / Ross A Edwards / Greg L Hura / Andrew T Xiao / John A Tainer / Michael J Hendzel / J N Mark Glover / ; 要旨: DNA double strand break (DSB) responses depend on the sequential actions of the E3 ubiquitin ligases RNF8 and RNF168 plus E2 ubiquitin-conjugating enzyme Ubc13 to specifically generate histone Lys-63-linked ubiquitin chains in DSB signaling. Here, we defined the activated RNF8-Ubc13∼ubiquitin complex by x-ray crystallography and its functional solution conformations by x-ray scattering, as tested by separation-of-function mutations imaged in cells by immunofluorescence. The collective results show that the RING E3 RNF8 targets E2 Ubc13 to DSB sites and plays a critical role in damage signaling by stimulating polyubiquitination through modulating conformations of ubiquitin covalently linked to the Ubc13 active site. Structure-guided separation-of-function mutations show that the RNF8 E2 stimulating activity is essential for DSB signaling in mammalian cells and is necessary for downstream recruitment of 53BP1 and BRCA1. Chromatin-targeted RNF168 rescues 53BP1 recruitment involved in non-homologous end joining but not BRCA1 recruitment for homologous recombination. These findings suggest an allosteric approach to targeting the ubiquitin-docking cleft at the E2-E3 interface for possible interventions in cancer and chronic inflammation, and moreover, they establish an independent RNF8 role in BRCA1 recruitment.

登録者

• Curtis Hodge
• Ross Edwards
• Mark Glover

モデル

• モデル #461: ; タイプ: mix / ソフトウェア: MES-FoXS / ダミー原子の半径: 1.90 A; Omokage検索でこの集合体の類似形状データを探す (詳細)
• モデル #462: ; タイプ: mix / ソフトウェア: MES-FoXS / ダミー原子の半径: 1.90 A; Omokage検索でこの集合体の類似形状データを探す (詳細)
• モデル #463: ; タイプ: mix / ソフトウェア: MES-FoXS / ダミー原子の半径: 1.90 A; Omokage検索でこの集合体の類似形状データを探す (詳細)
• モデル #464: ; タイプ: mix / ソフトウェア: MES-FoXS / ダミー原子の半径: 1.90 A; Omokage検索でこの集合体の類似形状データを探す (詳細)
• モデル #465: ; タイプ: mix / ソフトウェア: MES-FoXS / ダミー原子の半径: 1.90 A; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant): conjugated to Ubiquitin; Entity id: 304 / 305 / 306
• バッファ: 名称: HEPES / 濃度: 20.00 mM / pH: 6.8 / 組成: 200 mM NaCl, 0.01 mM, ZnSO4, and 1 mM DTT

要素 #304

名称: RNF8 / タイプ: protein / 記述: E3 ubiquitin-protein ligase RNF8 / 分子量: 17.618 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: O76064
配列:

GPLGSPEFQE HWALMEELNR SKKDFEAIIQ AKNKELEQTK EEKEKMQAQK EEVLSHMNDV LENELQCIIC SEYFIEAVTL NCAHSFCSYC INEWMKRKIE CPICRKDIKS KTYSLVLDNC INKMVNNLSS EVKERRIVLI RERKAKRLF

要素 #305

名称: Ubc13 - C87K, K92A / タイプ: protein
記述: Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)
分子量: 17.89 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: P61088
配列:

GPLGSPEFMA GLPRRIIKET QRLLAEPVPG IKAEPDESNA RYFHVVIAGP QDSPFEGGTF KLELFLPEEY PMAAPKVRFM TKIYHPNVDK LGRIKLDILA DKWSPALQIR TVLLSIQALL SAPNPDDPLA NDVAEQWKTN EAQAIETARA WTRLYAMNNI

要素 #306

名称: UBC / タイプ: protein / 記述: Polyubiquitin-C / 分子量: 8.565 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: P0CG48
配列:

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

実験情報

• ビーム: 設備名称: Advanced Light Source (ALS) 12.3.1 (SIBYLS) / 地域: Berkeley, CA / 国: USA / 線源: X-ray synchrotron / 波長: 0.103 Å
• 検出器: 名称: Pilatus 2M

スキャン

タイトル: Wild type RNF8/Ubc13 (C87K K92A)/Ubiquitin complex
測定日: 2015年9月8日 / 単位: 1/nm /

	Min	Max
Q	0.1393	4.0962

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 586 /

	Min	Max
Q	0.003482	0.299312
P(R) point	1	586
R	0	188.5

結果

カーブのタイプ: single_conc /

	実験値	Porod
分子量	66 kDa	-
体積	-	119.05 nm3

	P(R)	Guinier
前方散乱 I0	665.1	662.4
慣性半径, Rg	4.63 nm	4.45 nm

	Min	Max
D	-	18.85
Guinier point	2	14