+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13539 | ||||||||||||
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タイトル | S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II) | ||||||||||||
マップデータ | Composite cryo-EM density map for the budding yeast CMG-Csm3-Tof1-Mrc1-Ctf4-PolE-SCF(Dia2) complex on double-stranded DNA (conformation II), produced using the Phenix combine_focused_maps program | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / establishment of sister chromatid cohesion / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA-templated DNA replication maintenance of fidelity ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / establishment of sister chromatid cohesion / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA-templated DNA replication maintenance of fidelity / 遺伝子変換 / maintenance of DNA repeat elements / septin ring assembly / Unwinding of DNA / invasive growth in response to glucose limitation / replication fork arrest / DNA replication initiation / Cul8-RING ubiquitin ligase complex / protein-containing complex disassembly / meiotic chromosome segregation / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / nuclear DNA replication / MCM complex binding / GINS complex / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nucleotide-excision repair, DNA gap filling / SUMO binding / mitotic DNA replication / regulation of exit from mitosis / DNA replication proofreading / Antigen processing: Ubiquitination & Proteasome degradation / Activation of the pre-replicative complex / CMG complex / single-stranded DNA 3'-5' DNA exonuclease activity / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / nuclear pre-replicative complex / vacuolar acidification / kinetochore assembly / Activation of ATR in response to replication stress / MCM complex / regulation of metabolic process / DNA replication preinitiation complex / exit from mitosis / double-strand break repair via break-induced replication / mitotic DNA replication checkpoint signaling / replication fork protection complex / mitotic DNA replication initiation / single-stranded DNA helicase activity / positive regulation of glucose transmembrane transport / protein neddylation / mitotic intra-S DNA damage checkpoint signaling / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エンドデオキシリボヌクレアーゼ / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / mitochondrial fusion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / DNA strand elongation involved in DNA replication / SCF複合体 / mitotic sister chromatid cohesion / leading strand elongation / nuclear chromosome / DNA unwinding involved in DNA replication / replication fork processing / DNA replication origin binding / nuclear replication fork / cullin family protein binding / regulation of DNA replication / subtelomeric heterochromatin formation / DNA replication initiation / 細胞内膜系 / regulation of protein-containing complex assembly / negative regulation of cytoplasmic translation / error-prone translesion synthesis / heterochromatin formation / base-excision repair, gap-filling / regulation of mitotic cell cycle / DNA helicase activity / meiotic cell cycle / DNA複製 / helicase activity / G1/S transition of mitotic cell cycle / 塩基除去修復 / DNA-templated DNA replication / 動原体 / nucleosome assembly / double-strand break repair via nonhomologous end joining / G2/M transition of mitotic cell cycle / double-strand break repair / single-stranded DNA binding / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / ubiquitin-dependent protein catabolic process / double-stranded DNA binding 類似検索 - 分子機能 | ||||||||||||
生物種 | DNA molecule (デオキシリボ核酸) / Saccharomyces cerevisiae (パン酵母) / 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: 3.2 Å | ||||||||||||
データ登録者 | Jenkyn-Bedford M / Yeeles JTP / Deegan TD | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: Nature / 年: 2021 タイトル: A conserved mechanism for regulating replisome disassembly in eukaryotes. 著者: Michael Jenkyn-Bedford / Morgan L Jones / Yasemin Baris / Karim P M Labib / Giuseppe Cannone / Joseph T P Yeeles / Tom D Deegan / 要旨: Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase. Despite being driven by evolutionarily ...Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase. Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCF in budding yeast, CUL2 in metazoa), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA. However, it is unknown how SCF and CUL2 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity. | ||||||||||||
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_13539.map.gz | 168 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13539-v30.xml emd-13539.xml | 49.7 KB 49.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_13539.png | 95.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13539 | 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_13539.map.gz / 形式: CCP4 / 大きさ: 202.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Composite cryo-EM density map for the budding yeast CMG-Csm3-Tof1-Mrc1-Ctf4-PolE-SCF(Dia2) complex on double-stranded DNA (conformation II), produced using the Phenix combine_focused_maps program | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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 : Budding yeast replisome on double-stranded DNA engaged with SCF(D...
+超分子 #1: Budding yeast replisome on double-stranded DNA engaged with SCF(D...
+超分子 #2: DNA
+超分子 #3: Replisome
+分子 #1: DNA replication licensing factor MCM2
+分子 #2: DNA replication licensing factor MCM3
+分子 #3: DNA replication licensing factor MCM4
+分子 #4: Minichromosome maintenance protein 5
+分子 #5: DNA replication licensing factor MCM6
+分子 #6: DNA replication licensing factor MCM7
+分子 #7: DNA replication complex GINS protein PSF1
+分子 #8: DNA replication complex GINS protein PSF2
+分子 #9: DNA replication complex GINS protein PSF3
+分子 #10: DNA replication complex GINS protein SLD5
+分子 #11: Cell division control protein 45,Cell division control protein 45
+分子 #12: DNA polymerase alpha-binding protein
+分子 #15: Suppressor of kinetochore protein 1
+分子 #16: Protein DIA2
+分子 #17: DNA polymerase epsilon catalytic subunit A
+分子 #18: DNA polymerase epsilon subunit B
+分子 #19: Topoisomerase 1-associated factor 1
+分子 #20: Chromosome segregation in meiosis protein 3
+分子 #13: Leading strand template DNA
+分子 #14: Lagging strand template DNA
+分子 #21: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+分子 #22: MAGNESIUM ION
+分子 #23: ZINC ION
-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: 7.6 |
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 前処理 - タイプ: GLOW DISCHARGE / 詳細: 15 mA |
凍結 | 凍結剤: ETHANE / 詳細: Manual plunger. |
-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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 0.4 µm / 倍率(公称値): 81000 |
特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 実像数: 12730 / 平均露光時間: 4.0 sec. / 平均電子線量: 38.8 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: 2160000 |
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CTF補正 | ソフトウェア - 名称: RELION (ver. 3) |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 3) |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 3) |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3) 詳細: Composite map produced from individual cryo-EM density maps (resolutions 3.2 - 4.0 A) using Phenix combine_focused_maps. See publication for details. 使用した粒子像数: 369254 |