+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-38099 | |||||||||
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タイトル | Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | RNF168 / nucleosome / H2AK13/15 ubiquitination / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / Formation of the ternary complex, and subsequently, the 43S complex / DNA repair-dependent chromatin remodeling ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / Formation of the ternary complex, and subsequently, the 43S complex / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion / Ribosomal scanning and start codon recognition / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / K63-linked polyubiquitin modification-dependent protein binding / Translation initiation complex formation / negative regulation of transcription elongation by RNA polymerase II / protein monoubiquitination / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / ubiquitin conjugating enzyme activity / Selenocysteine synthesis / protein K63-linked ubiquitination / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of BMP signaling pathway / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / negative regulation of megakaryocyte differentiation / nucleosome binding / Major pathway of rRNA processing in the nucleolus and cytosol / protein autoubiquitination / protein K48-linked ubiquitination / protein localization to CENP-A containing chromatin / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Chromatin modifying enzymes / interstrand cross-link repair / Replacement of protamines by nucleosomes in the male pronucleus / SUMOylation of DNA damage response and repair proteins / CENP-A containing nucleosome / Packaging Of Telomere Ends / ubiquitin ligase complex / cytosolic ribosome / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Prevention of phagosomal-lysosomal fusion / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Endosomal Sorting Complex Required For Transport (ESCRT) / TICAM1,TRAF6-dependent induction of TAK1 complex / Membrane binding and targetting of GAG proteins / Inhibition of DNA recombination at telomere / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of FZD by ubiquitination / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / telomere organization / p75NTR recruits signalling complexes / Meiotic synapsis / APC/C:Cdc20 mediated degradation of Cyclin B / 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 / positive regulation of DNA repair / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / InlA-mediated entry of Listeria monocytogenes into host cells / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Regulation of pyruvate metabolism / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Assembly of the ORC complex at the origin of replication / Pexophagy / Activated NOTCH1 Transmits Signal to the Nucleus 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: 3.27 Å | |||||||||
データ登録者 | Ai HS / Tong ZB / Deng ZH / Pan M / Liu L | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Biorxiv / 年: 2024 タイトル: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168 著者: Ai H / Tong Z / Deng Z / Shi Q / Tao S / Liang J / Sun M / Wu X / Zheng Q / Liang L / Li JB / Gao S / Tian C / Liu L / Pan M | |||||||||
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_38099.map.gz | 3.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-38099-v30.xml emd-38099.xml | 28.6 KB 28.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_38099_fsc.xml | 9.1 KB | 表示 | FSCデータファイル |
画像 | emd_38099.png | 67.5 KB | ||
マスクデータ | emd_38099_msk_1.map | 64 MB | マスクマップ | |
Filedesc metadata | emd-38099.cif.gz | 7 KB | ||
その他 | emd_38099_additional_1.map.gz emd_38099_additional_2.map.gz emd_38099_half_map_1.map.gz emd_38099_half_map_2.map.gz | 616.3 KB 2.6 MB 49.6 MB 49.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-38099 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38099 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_38099_validation.pdf.gz | 721.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_38099_full_validation.pdf.gz | 720.9 KB | 表示 | |
XML形式データ | emd_38099_validation.xml.gz | 15.2 KB | 表示 | |
CIF形式データ | emd_38099_validation.cif.gz | 20.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38099 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38099 | HTTPS FTP |
-関連構造データ
関連構造データ | 8x7iMC 8x7jC 8x7kC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_38099.map.gz / 形式: CCP4 / 大きさ: 64 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: 1.074 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_38099_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 |
-追加マップ: Local cryo-EM map of RNF168-UbcH5c at a resolution of 3.62 angstrom
ファイル | emd_38099_additional_1.map | ||||||||||||
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注釈 | Local cryo-EM map of RNF168-UbcH5c at a resolution of 3.62 angstrom | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Cryo-EM map of RNF168/UbcH5c-Ub/nucleosome at a resolution of...
ファイル | emd_38099_additional_2.map | ||||||||||||
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注釈 | Cryo-EM map of RNF168/UbcH5c-Ub/nucleosome at a resolution of 3.12 angstrom | ||||||||||||
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_38099_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: #2
ファイル | emd_38099_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 : RNF168/UbcH5c-Ub/nucleosomes determined by intein-based E2-Ub-NCP...
+超分子 #1: RNF168/UbcH5c-Ub/nucleosomes determined by intein-based E2-Ub-NCP...
+分子 #1: Histone H3.2
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2A type 1-B/E
+分子 #7: Histone H2B type 1-K
+分子 #8: Ubiquitin-conjugating enzyme E2 D3
+分子 #9: E3 ubiquitin-protein ligase RNF168
+分子 #10: Ubiquitin
+分子 #5: DNA (147-MER)
+分子 #6: DNA (147-MER)
+分子 #11: ZINC ION
-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 |
-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: 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 | 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): 2.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |