+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13537 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation I) | ||||||||||||
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 I), produced using the Phenix combine_focused_maps progam | ||||||||||||
試料 |
| ||||||||||||
キーワード | Genome stability / DNA replication / Ubiquitination / termination / replisome / cryo-EM / CMG / SCF(Dia2) / REPLICATION | ||||||||||||
機能・相同性 | 機能・相同性情報 mitotic DNA replication termination / maintenance of DNA repeat elements / DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / invasive growth in response to glucose limitation / replication fork arrest / cell cycle / DNA replication initiation / meiotic chromosome segregation ...mitotic DNA replication termination / maintenance of DNA repeat elements / DNA-templated DNA replication maintenance of fidelity / gene conversion / Unwinding of DNA / invasive growth in response to glucose limitation / replication fork arrest / cell cycle / DNA replication initiation / meiotic chromosome segregation / protein-containing complex disassembly / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / MCM complex binding / GINS complex / nuclear DNA replication / mitotic DNA replication preinitiation complex assembly / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / SUMO binding / Activation of the pre-replicative complex / mitotic DNA replication / CMG complex / DNA replication checkpoint signaling / nuclear pre-replicative complex / nucleotide-excision repair, DNA gap filling / establishment of mitotic sister chromatid cohesion / single-stranded DNA 3'-5' DNA exonuclease activity / Activation of ATR in response to replication stress / DNA replication preinitiation complex / MCM complex / replication fork protection complex / DNA replication proofreading / Termination of translesion DNA synthesis / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / mitotic intra-S DNA damage checkpoint signaling / silent mating-type cassette heterochromatin formation / DNA strand elongation involved in DNA replication / 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 / SCF ubiquitin ligase complex / mitotic sister chromatid cohesion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / 3'-5' DNA helicase activity / leading strand elongation / DNA unwinding involved in DNA replication / replication fork processing / nuclear replication fork / regulation of DNA replication / DNA replication origin binding / cullin family protein binding / Dual incision in TC-NER / subtelomeric heterochromatin formation / DNA replication initiation / error-prone translesion synthesis / base-excision repair, gap-filling / DNA helicase activity / replication fork / meiotic cell cycle / helicase activity / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / single-stranded DNA binding / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / ubiquitin-dependent protein catabolic process / DNA helicase / DNA replication / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / protein ubiquitination / DNA repair / mRNA binding / nucleotide binding / chromatin binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | DNA molecule (その他) / 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 | ||||||||||||
資金援助 | 英国, 3件
| ||||||||||||
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 |
|
-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_13537.map.gz | 162.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-13537-v30.xml emd-13537.xml | 50.4 KB 50.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_13537.png | 89.3 KB | ||
Filedesc metadata | emd-13537.cif.gz | 16.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13537 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13537_validation.pdf.gz | 515.4 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_13537_full_validation.pdf.gz | 514.9 KB | 表示 | |
XML形式データ | emd_13537_validation.xml.gz | 7.4 KB | 表示 | |
CIF形式データ | emd_13537_validation.cif.gz | 8.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13537 | 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_13537.map.gz / 形式: CCP4 / 大きさ: 202.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 I), produced using the Phenix combine_focused_maps progam | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 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
-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: DNA helicase
+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: E3 ubiquitin ligase complex SCF subunit
+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 |
---|---|
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 |
---|---|
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 / 前処理 - 時間: 5 sec. / 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 |
---|---|
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 |
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 |
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): 2.2 µm / 最小 デフォーカス(公称値): 0.4 µm / 倍率(公称値): 81000 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |