+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8pp7 | ||||||
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タイトル | human RYBP-PRC1 bound to mononucleosome | ||||||
要素 |
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キーワード | GENE REGULATION / ncPRC1 complex / nucleosome / H2A / histones / RING1B / BMI1 / heterodimer / E3 ligase / K119 | ||||||
機能・相同性 | 機能・相同性情報 histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / Condensation of Prophase Chromosomes / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RNA Polymerase I Promoter Escape / polytene chromosome band / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / Ub-specific processing proteases / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / larval somatic muscle development / Senescence-Associated Secretory Phenotype (SASP) / RING-like zinc finger domain binding / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / UCH proteinases / PRC1 complex / sex chromatin / segment specification / rostrocaudal neural tube patterning / polytene chromosome / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / SUMOylation of chromatin organization proteins / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / germ cell development / humoral immune response / hemopoiesis / negative regulation of apoptotic signaling pathway / MLL1 complex / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / nucleosomal DNA binding / Regulation of PTEN gene transcription / epigenetic regulation of gene expression / SUMOylation of transcription cofactors / promoter-specific chromatin binding / apoptotic signaling pathway / RING-type E3 ubiquitin transferase / euchromatin / brain development / negative regulation of DNA-binding transcription factor activity / heterochromatin formation / positive regulation of fibroblast proliferation / structural constituent of chromatin / chromosome / nucleosome / ubiquitin protein ligase activity / nucleosome assembly / chromatin organization / regulation of gene expression / mitotic cell cycle / gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / chromatin remodeling / nuclear body / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Drosophila melanogaster (キイロショウジョウバエ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.91 Å | ||||||
データ登録者 | Ciapponi, M. / Benda, C. / Mueller, J. | ||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1. 著者: Maria Ciapponi / Elena Karlukova / Sven Schkölziger / Christian Benda / Jürg Müller / 要旨: Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified ...Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8pp7.cif.gz | 426.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8pp7.ent.gz | 313.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8pp7.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8pp7_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8pp7_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 8pp7_validation.xml.gz | 42.7 KB | 表示 | |
CIF形式データ | 8pp7_validation.cif.gz | 67 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pp/8pp7 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/8pp7 | HTTPS FTP |
-関連構造データ
関連構造データ | 17797MC 8pp6C M: このデータのモデリングに利用したマップデータ 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
-集合体
登録構造単位 |
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-要素
-タンパク質 , 6種, 12分子 KMLNAEBFCGDH
#1: タンパク質 | 分子量: 38152.359 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BMI1, PCGF4, RNF51 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P35226 #2: タンパク質 | 分子量: 38062.707 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RNF2, BAP1, DING, HIPI3, RING1B / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q99496, RING-type E3 ubiquitin transferase #3: タンパク質 | 分子量: 15289.904 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: H3_1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A7L0PXJ3 #4: タンパク質 | 分子量: 11521.611 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: His4r, BcDNA:RH52884, Dmel\CG3379, FBtr0082962, H4r, His4-88CD, His4R, CG3379, Dmel_CG3379 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A0B4KFZ9 #5: タンパク質 | 分子量: 13257.529 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A: ...遺伝子: His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P84051 #6: タンパク質 | 分子量: 13727.064 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Drosophila melanogaster (キイロショウジョウバエ) 遺伝子: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B: ...遺伝子: His2B, His2B:CG17949, CG17949, His2B:CG33868, CG33868, His2B:CG33870, CG33870, His2B:CG33872, CG33872, His2B:CG33874, CG33874, His2B:CG33876, CG33876, His2B:CG33878, CG33878, His2B:CG33880, CG33880, His2B:CG33882, CG33882, His2B:CG33884, CG33884, His2B:CG33886, CG33886, His2B:CG33888, CG33888, His2B:CG33890, CG33890, His2B:CG33892, CG33892, His2B:CG33894, CG33894, His2B:CG33896, CG33896, His2B:CG33898, CG33898, His2B:CG33900, CG33900, His2B:CG33902, CG33902, His2B:CG33904, CG33904, His2B:CG33906, CG33906, His2B:CG33908, CG33908, His2B:CG33910, CG33910 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02283 |
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-DNA鎖 , 2種, 2分子 JI
#7: DNA鎖 | 分子量: 76716.836 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) |
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#8: DNA鎖 | 分子量: 76481.609 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) |
-非ポリマー , 1種, 8分子
#9: 化合物 | ChemComp-ZN / |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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分子量 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 | ||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 278 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 電子線照射量: 58.6 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.91 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 146136 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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