+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-37503 | |||||||||
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タイトル | Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome | |||||||||
マップデータ | Main map at a resolution of 3.05 angstrom | |||||||||
試料 |
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キーワード | nucleosome complex / USP16 / H2AK119Ub / NUCLEAR PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 mitotic nuclear division / histone H2A deubiquitinase activity / monoubiquitinated protein deubiquitination / positive regulation of translational elongation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / ribosomal small subunit binding / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity ...mitotic nuclear division / histone H2A deubiquitinase activity / monoubiquitinated protein deubiquitination / positive regulation of translational elongation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / ribosomal small subunit binding / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / positive regulation of ribosome biogenesis / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / ubiquitin binding / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / gene expression / antibacterial humoral response / histone binding / Oxidative Stress Induced Senescence / protein homotetramerization / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / transcription coactivator activity / killing of cells of another organism / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of cell population proliferation / cysteine-type endopeptidase activity / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex 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: 3.05 Å | |||||||||
データ登録者 | Ai HS / He ZZ / Deng ZH / Liu L | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. 著者: Huasong Ai / Zaozhen He / Zhiheng Deng / Guo-Chao Chu / Qiang Shi / Zebin Tong / Jia-Bin Li / Man Pan / Lei Liu / 要旨: Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in ...Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in transcription repression, is dynamically regulated by the opposing activities of Polycomb repressive complex 1 (PRC1) and nucleosome deubiquitinases including the primary human USP16 and Polycomb repressive deubiquitinase (PR-DUB) complex. Recently, the catalytic mechanism for the multi-subunit PR-DUB complex has been described, but how the single-subunit USP16 recognizes the H2AK119Ub nucleosome and cleaves the ubiquitin (Ub) remains unknown. Here we report the cryo-EM structure of USP16-H2AK119Ub nucleosome complex, which unveils a fundamentally distinct mode of H2AK119Ub deubiquitination compared to PR-DUB, encompassing the nucleosome recognition pattern independent of the H2A-H2B acidic patch and the conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail. Our work highlights the mechanism diversity of H2AK119Ub deubiquitination and provides a structural framework for understanding the disease-causing mutations of USP16. | |||||||||
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_37503.map.gz | 4.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-37503-v30.xml emd-37503.xml | 26.3 KB 26.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_37503_fsc.xml | 9.1 KB | 表示 | FSCデータファイル |
画像 | emd_37503.png | 162.3 KB | ||
マスクデータ | emd_37503_msk_1.map | 64 MB | マスクマップ | |
Filedesc metadata | emd-37503.cif.gz | 7 KB | ||
その他 | emd_37503_additional_1.map.gz emd_37503_additional_2.map.gz emd_37503_half_map_1.map.gz emd_37503_half_map_2.map.gz | 1.2 MB 4.4 MB 49.7 MB 49.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-37503 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37503 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_37503_validation.pdf.gz | 725.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_37503_full_validation.pdf.gz | 725.4 KB | 表示 | |
XML形式データ | emd_37503_validation.xml.gz | 15.2 KB | 表示 | |
CIF形式データ | emd_37503_validation.cif.gz | 20.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37503 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37503 | HTTPS FTP |
-関連構造データ
関連構造データ | 8wg5MC 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_37503.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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注釈 | Main map at a resolution of 3.05 angstrom | ||||||||||||||||||||
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_37503_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: USP16-Ub local map at a resolution of 3.05 angstrom
ファイル | emd_37503_additional_1.map | ||||||||||||
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注釈 | USP16-Ub local map at a resolution of 3.05 angstrom | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: USP16-H2AK119Ub complex map at a resolution of 3.35 angstrom
ファイル | emd_37503_additional_2.map | ||||||||||||
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注釈 | USP16-H2AK119Ub complex map at a resolution of 3.35 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_37503_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_37503_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 : Complex of USP16 bound to H2AK119Ub nucleosome
全体 | 名称: Complex of USP16 bound to H2AK119Ub nucleosome |
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要素 |
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-超分子 #1: Complex of USP16 bound to H2AK119Ub nucleosome
超分子 | 名称: Complex of USP16 bound to H2AK119Ub nucleosome / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#8 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Ubiquitin carboxyl-terminal hydrolase 16
分子 | 名称: Ubiquitin carboxyl-terminal hydrolase 16 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: ubiquitinyl hydrolase 1 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 93.70825 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MGKKRTKGKT VPIDDSSETL EPVCRHIRKG LEQGNLKKAL VNVEWNICQD CKTDNKVKDK AEEETEEKPS VWLCLKCGHQ GCGRNSQEQ HALKHYLTPR SEPHCLVLSL DNWSVWCYVC DNEVQYCSSN QLGQVVDYVR KQASITTPKP AEKDNGNIEL E NKKLEKES ...文字列: MGKKRTKGKT VPIDDSSETL EPVCRHIRKG LEQGNLKKAL VNVEWNICQD CKTDNKVKDK AEEETEEKPS VWLCLKCGHQ GCGRNSQEQ HALKHYLTPR SEPHCLVLSL DNWSVWCYVC DNEVQYCSSN QLGQVVDYVR KQASITTPKP AEKDNGNIEL E NKKLEKES KNEQEREKKE NMAKENPPMN SPCQITVKGL SNLGNTCFFN AVMQNLSQTP VLRELLKEVK MSGTIVKIEP PD LALTEPL EINLEPPGPL TLAMSQFLNE MQETKKGVVT PKELFSQVCK KAVRFKGYQQ QDSQELLRYL LDGMRAEEHQ RVS KGILKA FGNSTEKLDE ELKNKVKDYE KKKSMPSFVD RIFGGELTSM IMCDQCRTVS LVHESFLDLS LPVLDDQSGK KSVN DKNLK KTVEDEDQDS EEEKDNDSYI KERSDIPSGT SKHLQKKAKK QAKKQAKNQR RQQKIQGKVL HLNDICTIDH PEDSE YEAE MSLQGEVNIK SNHISQEGVM HKEYCVNQKD LNGQAKMIES VTDNQKSTEE VDMKNINMDN DLEVLTSSPT RNLNGA YLT EGSNGEVDIS NGFKNLNLNA ALHPDEINIE ILNDSHTPGT KVYEVVNEDP ETAFCTLANR EVFNTDECSI QHCLYQF TR NEKLRDANKL LCEVCTRRQC NGPKANIKGE RKHVYTNAKK QMLISLAPPV LTLHLKRFQQ AGFNLRKVNK HIKFPEIL D LAPFCTLKCK NVAEENTRVL YSLYGVVEHS GTMRSGHYTA YAKARTANSH LSNLVLHGDI PQDFEMESKG QWFHISDTH VQAVPTTKVL NSQAYLLFYE RIL UniProtKB: Ubiquitin carboxyl-terminal hydrolase 16 |
-分子 #2: Histone H3.1
分子 | 名称: Histone H3.1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 11.562577 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: KPHRYRPGTV ALREIRRYQK STELLIRKLP FQRLVREIAQ DFKTDLRFQS SAVMALQEAC EAYLVGLFED TNLCAIHAKR VTIMPKDIQ LARRIRGER UniProtKB: Histone H3.1 |
-分子 #3: Histone H4
分子 | 名称: Histone H4 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 9.010534 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: RDNIQGITKP AIRRLARRGG VKRISGLIYE ETRGVLKVFL ENVIRDAVTY TEHAKRKTVT AMDVVYALKR QGRTLYGFG UniProtKB: Arachidonate 15-lipoxygenase |
-分子 #4: Histone H2A type 1-B/E
分子 | 名称: Histone H2A type 1-B/E / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 12.141195 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG RVTIAQGGVL PNIQAVLLPK CT UniProtKB: Histone H2A type 1-B/E |
-分子 #5: Histone H2B type 1-K
分子 | 名称: Histone H2B type 1-K / タイプ: protein_or_peptide / ID: 5 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 10.477994 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSA UniProtKB: Histone H2B type 1-K |
-分子 #8: Ubiquitin B
分子 | 名称: Ubiquitin B / タイプ: protein_or_peptide / ID: 8 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 8.622922 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC UniProtKB: Ubiquitin B |
-分子 #6: DNA (147-MER)
分子 | 名称: DNA (147-MER) / タイプ: dna / ID: 6 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 45.604047 KDa |
配列 | 文字列: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT) ...文字列: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG) |
-分子 #7: DNA (147-MER)
分子 | 名称: DNA (147-MER) / タイプ: dna / ID: 7 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 45.145754 KDa |
配列 | 文字列: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC) ...文字列: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT) |
-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): 1.8 µm / 最小 デフォーカス(公称値): 1.3 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |