+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-21707 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome | |||||||||
![]() | half map-1 for 2:1 | |||||||||
![]() |
| |||||||||
機能・相同性 | ![]() protein localization to pericentric heterochromatin / regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / CAF-1 complex / negative regulation of keratinocyte differentiation ...protein localization to pericentric heterochromatin / regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / CAF-1 complex / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / random inactivation of X chromosome / primary miRNA binding / ubiquitin-modified histone reader activity / regulatory ncRNA-mediated heterochromatin formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / facultative heterochromatin formation / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / positive regulation of cell cycle G1/S phase transition / negative regulation of cardiac muscle cell proliferation / NURF complex / NuRD complex / regulation of cell fate specification / negative regulation of stem cell population maintenance / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / chromatin silencing complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / RSC-type complex / Transcription of E2F targets under negative control by DREAM complex / pronucleus / cardiac muscle hypertrophy in response to stress / Polo-like kinase mediated events / synaptic transmission, GABAergic / G0 and Early G1 / positive regulation of dendrite development / histone H3 methyltransferase activity / lncRNA binding / cardiac muscle cell proliferation / Cyclin E associated events during G1/S transition / SUMOylation of chromatin organization proteins / histone methyltransferase complex / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / negative regulation of gene expression, epigenetic / spinal cord development / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / histone methyltransferase activity / ATPase complex / Sin3-type complex / Cyclin A:Cdk2-associated events at S phase entry / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / subtelomeric heterochromatin formation / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / ribonucleoprotein complex binding / positive regulation of epithelial to mesenchymal transition / Deposition of new CENPA-containing nucleosomes at the centromere / keratinocyte differentiation / transcription coregulator activity / Maturation of protein E / Maturation of protein E / spleen development / ER Quality Control Compartment (ERQC) / protein localization to chromatin / Myoclonic epilepsy of Lafora / enzyme activator activity / Regulation of TP53 Activity through Acetylation / FLT3 signaling by CBL mutants / Regulation of PTEN gene transcription / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
![]() | Kasinath V / Nogales E / Beck C / Sauer P / Poepsel S / Kosmatka J / Faini M / Toso D / Aebersold R | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() タイトル: JARID2 and AEBP2 regulate PRC2 in the presence of H2AK119ub1 and other histone modifications. 著者: Vignesh Kasinath / Curtis Beck / Paul Sauer / Simon Poepsel / Jennifer Kosmatka / Marco Faini / Daniel Toso / Ruedi Aebersold / Eva Nogales / ![]() ![]() ![]() 要旨: Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) cooperate to determine cell identity by epigenetic gene expression regulation. However, the mechanism of PRC2 recruitment by means of recognition ...Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) cooperate to determine cell identity by epigenetic gene expression regulation. However, the mechanism of PRC2 recruitment by means of recognition of PRC1-mediated H2AK119ub1 remains poorly understood. Our PRC2 cryo-electron microscopy structure with cofactors JARID2 and AEBP2 bound to a H2AK119ub1-containing nucleosome reveals a bridge helix in EZH2 that connects the SET domain, H3 tail, and nucleosomal DNA. JARID2 and AEBP2 each interact with one ubiquitin and the H2A-H2B surface. JARID2 stimulates PRC2 through interactions with both the polycomb protein EED and the H2AK119-ubiquitin, whereas AEBP2 has an additional scaffolding role. The presence of these cofactors partially overcomes the inhibitory effect that H3K4me3 and H3K36me3 exert on core PRC2 (in the absence of cofactors). Our results support a key role for JARID2 and AEBP2 in the cross-talk between histone modifications and PRC2 activity. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
-
ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 124.9 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 58.2 KB 58.2 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 13.6 KB | 表示 | ![]() |
画像 | ![]() | 117.7 KB | ||
マスクデータ | ![]() ![]() | 216 MB 216 MB | ![]() | |
その他 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 125 MB 190.1 MB 189.9 MB 124.5 MB 149 MB 148.8 MB 149.1 MB 148.7 MB 124.4 MB 124.8 MB 171.4 MB 171 MB 171 MB 170.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | half map-1 for 2:1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.1492 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
+マスク #1
+マスク #2
+追加マップ: local res filtered map 2:1 (Bfac = 50)
+追加マップ: data set 2 half 1
+追加マップ: data set 2 half 2
+追加マップ: data set 2 loc res filtered (bfac 50)
+追加マップ: body 1 half map 1 multibody
+追加マップ: body 2 half map 1 multibody
+追加マップ: body 1 half map 2 multibody
+追加マップ: body 2 half map 2 multibody
+追加マップ: body 1 local res filtered (Bfac = 50)
+追加マップ: body 2 local res filtered (Bfac = 50)
+追加マップ: half map-1 for 2:1
+追加マップ: half map-2 for 2:1
+ハーフマップ: half map 1 full refined map
+ハーフマップ: data set 2 half 1
-
試料の構成要素
+全体 : PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
+超分子 #1: PRC2-AEBP2-JARID2 bound to H2AK119ub1 nucleosome
+超分子 #2: PRC2-AEBP2-JARID2
+超分子 #3: H2AK119ub1 nucleosome
+分子 #1: Ubiquitin
+分子 #2: Polycomb protein SUZ12
+分子 #3: Polycomb protein EED
+分子 #4: Histone-binding protein RBBP4
+分子 #5: Histone-lysine N-methyltransferase EZH2
+分子 #6: Protein Jumonji
+分子 #7: Zinc finger protein AEBP2
+分子 #9: Histone H3.2
+分子 #10: Histone H4
+分子 #11: Histone H2A type 1
+分子 #12: Histone H2B 1.1
+分子 #8: DNA (314-MER)
+分子 #13: MAGNESIUM ION
+分子 #14: S-ADENOSYL-L-HOMOCYSTEINE
+分子 #15: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
緩衝液 | pH: 7.9 |
---|---|
グリッド | モデル: Quantifoil R2/2 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 278 K / 装置: FEI VITROBOT MARK IV |
-
電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (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: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |