+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23022 | |||||||||
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タイトル | Cryo-EM map of PRC2:EZH1-AEBP2 | |||||||||
マップデータ | Cryo-EM map of PRC2:EZH1-AEBP2 | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 protein localization to pericentric heterochromatin / [histone H3]-lysine27 N-trimethyltransferase / クロマチン / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation ...protein localization to pericentric heterochromatin / [histone H3]-lysine27 N-trimethyltransferase / クロマチン / CAF-1 complex / histone H3K27 trimethyltransferase activity / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / facultative heterochromatin formation / 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 / RSC-type complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / lncRNA binding / cardiac muscle cell proliferation / histone methyltransferase complex / ATPase complex / spinal cord development / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / Sin3-type complex / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / subtelomeric heterochromatin formation / histone deacetylase complex / G0 and Early G1 / enzyme activator activity / anatomical structure morphogenesis / ヘテロクロマチン / heterochromatin formation / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / spleen development / Regulation of TP53 Activity through Acetylation / methylated histone binding / cellular response to leukemia inhibitory factor / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / thymus development / liver development / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / ubiquitin binding / central nervous system development / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / 細胞分化 / hippocampus development / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / transcription corepressor activity / 染色体 / chromatin organization / メチル化 / histone binding / 遺伝子発現の調節 / Oxidative Stress Induced Senescence / cell population proliferation / Potential therapeutics for SARS / DNA複製 / chromosome, telomeric region / nuclear body / クロマチンリモデリング / 細胞周期 / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / クロマチン / 核小体 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II 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: 4.1 Å | |||||||||
データ登録者 | Grau DJ / Armache KJ | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Structures of monomeric and dimeric PRC2:EZH1 reveal flexible modules involved in chromatin compaction. 著者: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas Walz ...著者: Daniel Grau / Yixiao Zhang / Chul-Hwan Lee / Marco Valencia-Sánchez / Jenny Zhang / Miao Wang / Marlene Holder / Vladimir Svetlov / Dongyan Tan / Evgeny Nudler / Danny Reinberg / Thomas Walz / Karim-Jean Armache / 要旨: Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the ...Polycomb repressive complex 2 (PRC2) is a histone methyltransferase critical for maintaining gene silencing during eukaryotic development. In mammals, PRC2 activity is regulated in part by the selective incorporation of one of two paralogs of the catalytic subunit, EZH1 or EZH2. Each of these enzymes has specialized biological functions that may be partially explained by differences in the multivalent interactions they mediate with chromatin. Here, we present two cryo-EM structures of PRC2:EZH1, one as a monomer and a second one as a dimer bound to a nucleosome. When bound to nucleosome substrate, the PRC2:EZH1 dimer undergoes a dramatic conformational change. We demonstrate that mutation of a divergent EZH1/2 loop abrogates the nucleosome-binding and methyltransferase activities of PRC2:EZH1. Finally, we show that PRC2:EZH1 dimers are more effective than monomers at promoting chromatin compaction, and the divergent EZH1/2 loop is essential for this function, thereby tying together the methyltransferase, nucleosome-binding, and chromatin-compaction activities of PRC2:EZH1. We speculate that the conformational flexibility and the ability to dimerize enable PRC2 to act on the varied chromatin substrates it encounters in the cell. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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_23022.map.gz | 20.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23022-v30.xml emd-23022.xml | 16.8 KB 16.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_23022.png | 94.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23022 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23022 | HTTPS FTP |
-関連構造データ
-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_23022.map.gz / 形式: CCP4 / 大きさ: 22.2 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM map of PRC2:EZH1-AEBP2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : PRC2:EZH1-AEBP2
全体 | 名称: PRC2:EZH1-AEBP2 |
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要素 |
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-超分子 #1: PRC2:EZH1-AEBP2
超分子 | 名称: PRC2:EZH1-AEBP2 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
分子量 | 理論値: 299 KDa |
-分子 #1: EZH1
分子 | 名称: EZH1 / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: meipnpptsk citywkrkv k seymrlrq lk rlqanmg aka lyvanf akvq ektqi lneew kklr vqpvqs mkp vsghpfl kk ctiesifp g fasqhmlmr slntvalvpi myswsplqq n fmvedetv lc nipymgd evk eedetf ieel innyd ...文字列: meipnpptsk citywkrkv k seymrlrq lk rlqanmg aka lyvanf akvq ektqi lneew kklr vqpvqs mkp vsghpfl kk ctiesifp g fasqhmlmr slntvalvpi myswsplqq n fmvedetv lc nipymgd evk eedetf ieel innyd gkvhg eeem ipgsvl isd avflelv da lnqysdee e eghndtsdg kqddskedlp vtrkrkrha i egnkkssk kq fpndmif sai asmfpe ngvp ddmke ryrel tems dpnalp pqc tpnidgp na ksvqreqs l hsfhtlfcr rcfkydcflh pfhatpnvy k rknkeiki ep epcgtdc fll legake yaml hnprs kcsgr rrrr hhivsa scs nasasav ae tkegdsdr d tgndwasss seansrcqtp tkqkaspap p qlcvveap se pvewtga ees lfrvfh gtyf nnfcs iarll gtkt ckqvfq fav keslilk lp tdelmnps q kkkrkhrlw aahcrkiqlk kdnsstqvy n yqpcdhpd rp cdstcpc imt qnfcek fcqc npdcq nrfpg crck tqcntk qcp cylavre cd pdlcltcg a sehwdckvv sckncsiqrg lkkhlllap s dvagwgtf ik esvqkne fis eycgel isqd eadrr gkvyd kyms sflfnl nnd fvvdatr kg nkirfanh s vnpncyakv vmvngdhrig ifakraiqa g eelffdyr ys qadalky vgi eretdv l |
-分子 #2: EED
分子 | 名称: EED / タイプ: protein_or_peptide / ID: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: mserevstap agtdmpaak k qklssden sn pdlsgde ndd avsies gtnt erpdt ptntp napg rkswgk gkw kskkcky sf kcvnslke d hnqplfgvq fnwhskegdp lvfatvgsn r vtlyechs qg eirllqs yvd adaden fytc awtyd ...文字列: mserevstap agtdmpaak k qklssden sn pdlsgde ndd avsies gtnt erpdt ptntp napg rkswgk gkw kskkcky sf kcvnslke d hnqplfgvq fnwhskegdp lvfatvgsn r vtlyechs qg eirllqs yvd adaden fytc awtyd sntsh plla vagsrg iir iinpitm qc ikhyvghg n ainelkfhp rdpnlllsvs kdhalrlwn i qtdtlvai fg gveghrd evl sadydl lgek imscg mdhsl klwr inskrm mna ikesydy np nktnrpfi s qkihfpdfs trdihrnyvd cvrwlgdli l skscenai vc wkpgkme ddi dkikps esnv tilgr fdysq cdiw ymrfsm dfw qkmlalg nq vgklyvwd l evedphkak cttlthhkcg aairqtsfs r dssiliav cd dasiwrw drl r |
-分子 #3: SUZ12
分子 | 名称: SUZ12 / タイプ: protein_or_peptide / ID: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: mapqkhgggg gggsgpsag s ggggfggs aa vaaatas ggk sgggsc gggg sysas ssssa aaaa gaavlp vkk pkmehvq ad helflqaf e kptqiyrfl rtrnliapif lhrtltyms h rnsrtnik rk tfkvddm lsk vekmkg eqes hslsa ...文字列: mapqkhgggg gggsgpsag s ggggfggs aa vaaatas ggk sgggsc gggg sysas ssssa aaaa gaavlp vkk pkmehvq ad helflqaf e kptqiyrfl rtrnliapif lhrtltyms h rnsrtnik rk tfkvddm lsk vekmkg eqes hslsa hlqlt ftgf fhkndk psp nseneqn sv tlevllvk v chkkrkdvs cpirqvptgk kqvplnpdl n qtkpgnfp sl avssnef eps nshmvk sysl lfrvt rpgrr efng minget nen idvneel pa rrkrnred g ektfvaqmt vfdknrrlql ldgeyevam q emeecpis kk ratweti ldg krlppf etfs qgptl qftlr wtge tndkst api akplatr ns eslhqenk p gsvkptqti avkeslttdl qtrkekdtp n enrqklri fy qflynnn trq qteard dlhc pwctl ncrkl ysll khlklc hsr fifnyvy hp kgaridvs i necydgsya gnpqdihrqp gfafsrngp v krtpithi lv crpkrtk asm sefles edge veqqr tyssg hnrl yfhsdt clp lrpqeme vd sedekdpe w lrektitqi eefsdvnege kevmklwnl h vmkhgfia dn qmnhacm lfv enygqk iikk nlcrn fmlhl vsmh dfnlis ims idkavtk lr emqqklek g esaspanee iteeqngtan gfseinske k aletdsvs gv skqskkq kl |
-分子 #4: RBAP48
分子 | 名称: RBAP48 / タイプ: protein_or_peptide / ID: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: madkeaafdd aveervine e ykiwkknt pf lydlvmt hal ewpslt aqwl pdvtr pegkd fsih rlvlgt hts deqnhlv ia svqlpndd a qfdashyds ekgefggfgs vsgkieiei k inhegevn ra rympqnp cii atktps sdvl vfdyt ...文字列: madkeaafdd aveervine e ykiwkknt pf lydlvmt hal ewpslt aqwl pdvtr pegkd fsih rlvlgt hts deqnhlv ia svqlpndd a qfdashyds ekgefggfgs vsgkieiei k inhegevn ra rympqnp cii atktps sdvl vfdyt khpsk pdps gecnpd lrl rghqkeg yg lswnpnls g hllsasddh ticlwdisav pkegkvvda k tiftghta vv edvswhl lhe slfgsv addq klmiw dtrsn ntsk pshsvd aht aevncls fn pysefila t gsadktval wdlrnlklkl hsfeshkde i fqvqwsph ne tilassg tdr rlnvwd lski geeqs pedae dgpp ellfih ggh takisdf sw npnepwvi c svsednimq vwqmaeniyn dedpegsvd p egqgs |
-分子 #5: AEBP2
分子 | 名称: AEBP2 / タイプ: protein_or_peptide / ID: 5 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: mssdgeplsr mdsedsiss t imdvdsti ss grstpam mng qgstts sskn iaync cwdqc qacf nsspdl adh irsihvd gq rggvfvcl w kgckvyntp stsqswlqrh mlthsgdkp f kcvvggcn as fasqggl arh vpthfs qqns skvss ...文字列: mssdgeplsr mdsedsiss t imdvdsti ss grstpam mng qgstts sskn iaync cwdqc qacf nsspdl adh irsihvd gq rggvfvcl w kgckvyntp stsqswlqrh mlthsgdkp f kcvvggcn as fasqggl arh vpthfs qqns skvss qpkak eesp skagmn krr klknkrr rs lprphdff d aqtldairh raicfnlsah ieslgkghs v vfhstvia kr kedsgki kll lhwmpe dilp dvwvn eserh qlkt kvvhls klp kdtalll dp niyrtmpq k rlkr |
-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
濃度 | 0.05 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.9 構成要素:
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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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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 FIELDBright-field microscopy |
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: 47.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 3142334 |
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CTF補正 | ソフトウェア - 名称: CTFFIND (ver. 4) |
初期 角度割当 | タイプ: RANDOM ASSIGNMENT |
最終 3次元分類 | クラス数: 6 / ソフトウェア - 名称: RELION (ver. 3.0) |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 155809 |