+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11910 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Histone H3 recognition by nucleosome-bound PRC2 subunit EZH2. | |||||||||
マップデータ | Shows the Relion 3.0 postprocessed cryo-EM map of the EZH2sub-Nucsub structure, generated by particle subtraction and focused 3D refinement. | |||||||||
試料 |
| |||||||||
キーワード | Polycomb / nucleosome / histone methyltransferase / PRC2 / EZH2 / H3K36 / H3 tail / gene regulation / H3 / histone H3 / Polycomb Repressive Complex 2 / cryo-EM / nucleosome recognition / H3K36me2 / H3K36me3 | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of epidermal cell differentiation / : / : / transcription corepressor binding => GO:0001222 / subtelomeric heterochromatin formation => GO:0031509 / : / : / : / regulation of kidney development / hepatocyte homeostasis ...negative regulation of epidermal cell differentiation / : / : / transcription corepressor binding => GO:0001222 / subtelomeric heterochromatin formation => GO:0031509 / : / : / : / 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 / 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 / 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 / positive regulation of cell cycle G1/S phase transition / chromatin => GO:0000785 / negative regulation of G0 to G1 transition / ESC/E(Z) complex / chromatin silencing complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / RSC-type complex / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / positive regulation of dendrite development / histone H3 methyltransferase activity / lncRNA binding / SUMOylation of chromatin organization proteins / negative regulation of G1/S transition of mitotic cell cycle / G1 to G0 transition / negative regulation of gene expression, epigenetic / histone methyltransferase activity / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / negative regulation of cell differentiation / 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 / keratinocyte differentiation / protein localization to chromatin / enzyme activator activity / Regulation of PTEN gene transcription / methylated histone binding / liver regeneration / B cell differentiation / transcription corepressor binding / PRC2 methylates histones and DNA / positive regulation of MAP kinase activity / positive regulation of GTPase activity / Defective pyroptosis / stem cell differentiation / regulation of circadian rhythm / promoter-specific chromatin binding / hippocampus development / HCMV Early Events / PKMTs methylate histone lysines / protein modification process / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / G1/S transition of mitotic cell cycle / heterochromatin formation / chromatin DNA binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / structural constituent of chromatin / rhythmic process / chromosome / transcription corepressor activity / nucleosome / nucleosome assembly / chromatin organization / response to estradiol / chromosome, telomeric region / Oxidative Stress Induced Senescence / methylation / cell population proliferation / nuclear body / positive regulation of cell migration / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Xenopus laevis (アフリカツメガエル) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.4 Å | |||||||||
データ登録者 | Finogenova K / Benda C | |||||||||
資金援助 | ドイツ, 2件
| |||||||||
引用 | ジャーナル: Elife / 年: 2020 タイトル: Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3. 著者: Ksenia Finogenova / Jacques Bonnet / Simon Poepsel / Ingmar B Schäfer / Katja Finkl / Katharina Schmid / Claudia Litz / Mike Strauss / Christian Benda / Jürg Müller / 要旨: Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 ...Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes . Accordingly, H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
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 | emd_11910.map.gz | 6.1 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-11910-v30.xml emd-11910.xml | 24.6 KB 24.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_11910.png | 173.5 KB | ||
Filedesc metadata | emd-11910.cif.gz | 7.7 KB | ||
その他 | emd_11910_additional_1.map.gz | 2.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11910 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11910 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_11910.map.gz / 形式: CCP4 / 大きさ: 115.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Shows the Relion 3.0 postprocessed cryo-EM map of the EZH2sub-Nucsub structure, generated by particle subtraction and focused 3D refinement. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.746 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
-追加マップ: Phenix Resolve Cryo EM tool was used on...
ファイル | emd_11910_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Phenix Resolve Cryo EM tool was used on the Relion 3D refined map and half maps to generate a density modified map. This map showed significant improvement in the H3 tail. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : EM map of EZH2 on nucleosome obtained from signal particle subtra...
+超分子 #1: EM map of EZH2 on nucleosome obtained from signal particle subtra...
+超分子 #2: SUZ12 and EZH2
+超分子 #3: Histones
+超分子 #4: DNA
+分子 #1: Isoform 2 of Histone-lysine N-methyltransferase EZH2,Isoform 2 of...
+分子 #2: Polycomb protein SUZ12
+分子 #3: Histone H3.2
+分子 #4: Histone H4
+分子 #5: Histone H2A
+分子 #6: Histone H2B 1.1
+分子 #7: Widom601 DNA plus linker
+分子 #8: Widom601 DNA plus linker
+分子 #9: ZINC ION
+分子 #10: S-ADENOSYL-L-HOMOCYSTEINE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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: 7.8 |
---|---|
凍結 | 凍結剤: ETHANE-PROPANE |
-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 K2 SUMMIT (4k x 4k) 平均電子線量: 52.96 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: OTHER / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: 詳細: Other PDBs: 6T9L and 1AOI |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 45849 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |