+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13494 | ||||||||||||
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タイトル | H. sapiens replisome-CUL2/LRR1 complex | ||||||||||||
マップデータ | Locally filtered consensus refinement | ||||||||||||
試料 |
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キーワード | Genome stability / DNA replication / Ubiquitination / termination / replisome / cryo-EM / CMG / Cul2LRR1 / REPLICATION / DNA / polymerase / helicase | ||||||||||||
機能・相同性 | 機能・相同性情報 cellular response to bleomycin / DNA secondary structure binding / Switching of origins to a post-replicative state / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Unwinding of DNA / DNA replication initiation / epsilon DNA polymerase complex / cell cycle phase transition ...cellular response to bleomycin / DNA secondary structure binding / Switching of origins to a post-replicative state / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Unwinding of DNA / DNA replication initiation / epsilon DNA polymerase complex / cell cycle phase transition / cellular response to cisplatin / GINS complex / DNA strand elongation involved in mitotic DNA replication / mitotic DNA replication preinitiation complex assembly / nuclear origin of replication recognition complex / cellular response to hydroxyurea / alpha DNA polymerase:primase complex / mitotic DNA replication / cullin-RING-type E3 NEDD8 transferase / anaphase-promoting complex binding / cellular response to chemical stress / NEDD8 transferase activity / CMG complex / cullin-RING ubiquitin ligase complex / DNA replication checkpoint signaling / single-stranded 3'-5' DNA helicase activity / entrainment of circadian clock / single-stranded DNA 3'-5' DNA exonuclease activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / regulation of phosphorylation / MCM complex / DNA replication preinitiation complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / VCB complex / positive regulation of protein autoubiquitination / replication fork protection complex / mitotic DNA replication checkpoint signaling / mitotic DNA replication initiation / protein neddylation / double-strand break repair via break-induced replication / NEDD8 ligase activity / mitotic intra-S DNA damage checkpoint signaling / positive regulation of double-strand break repair / Cul5-RING ubiquitin ligase complex / negative regulation of response to oxidative stress / regulation of DNA-templated DNA replication initiation / ubiquitin-ubiquitin ligase activity / 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 / Cul4A-RING E3 ubiquitin ligase complex / single-stranded DNA helicase activity / SCF ubiquitin ligase complex / inner cell mass cell proliferation / Cul2-RING ubiquitin ligase complex / negative regulation of type I interferon production / nucleotide-excision repair, DNA gap filling / Cul4B-RING E3 ubiquitin ligase complex / DNA replication proofreading / ubiquitin ligase complex scaffold activity / DNA strand elongation involved in DNA replication / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / branching morphogenesis of an epithelial tube / DNA synthesis involved in DNA repair / cochlea development / G1/S-Specific Transcription / activation of protein kinase activity / leading strand elongation / replication fork processing / Prolactin receptor signaling / Apoptotic cleavage of cellular proteins / DNA unwinding involved in DNA replication / nuclear replication fork / protein monoubiquitination / mitotic G2 DNA damage checkpoint signaling / 3'-5' DNA helicase activity / DNA replication origin binding / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cullin family protein binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of double-strand break repair via homologous recombination / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / DNA replication initiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / cellular response to interleukin-4 / protein K48-linked ubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / Nuclear events stimulated by ALK signaling in cancer / error-prone translesion synthesis / Activation of ATR in response to replication stress / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV 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: 2.8 Å | ||||||||||||
データ登録者 | Jones MJ / Yeeles JTP | ||||||||||||
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_13494.map.gz | 140.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13494-v30.xml emd-13494.xml | 60.9 KB 60.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13494_fsc.xml | 18.3 KB | 表示 | FSCデータファイル |
画像 | emd_13494.png | 107.6 KB | ||
マスクデータ | emd_13494_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-13494.cif.gz | 17.3 KB | ||
その他 | emd_13494_additional_1.map.gz emd_13494_additional_2.map.gz emd_13494_half_map_1.map.gz emd_13494_half_map_2.map.gz | 123.3 MB 230.4 MB 226.9 MB 226.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13494 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13494 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13494_validation.pdf.gz | 965.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13494_full_validation.pdf.gz | 964.7 KB | 表示 | |
XML形式データ | emd_13494_validation.xml.gz | 21.5 KB | 表示 | |
CIF形式データ | emd_13494_validation.cif.gz | 28.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13494 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13494 | 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_13494.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Locally filtered consensus refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.072 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
-マスク #1
ファイル | emd_13494_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: consensus refinement
ファイル | emd_13494_additional_1.map | ||||||||||||
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注釈 | consensus refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: consensus refinement sharpened
ファイル | emd_13494_additional_2.map | ||||||||||||
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注釈 | consensus refinement sharpened | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: consensus refinement half 1
ファイル | emd_13494_half_map_1.map | ||||||||||||
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注釈 | consensus refinement half 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: consensus refinement half 2
ファイル | emd_13494_half_map_2.map | ||||||||||||
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注釈 | consensus refinement half 2 | ||||||||||||
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 : Human replisome engaged with CUL2-LRR1
+超分子 #1: Human replisome engaged with CUL2-LRR1
+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 replication licensing factor MCM5
+分子 #5: DNA replication licensing factor MCM6
+分子 #6: DNA replication licensing factor MCM7
+分子 #7: DNA polymerase epsilon subunit 2
+分子 #8: DNA polymerase epsilon catalytic subunit A
+分子 #9: Cell division control protein 45 homolog
+分子 #10: DNA replication complex GINS protein PSF1
+分子 #11: DNA replication complex GINS protein PSF2
+分子 #12: DNA replication complex GINS protein PSF3
+分子 #13: DNA replication complex GINS protein SLD5
+分子 #14: WD repeat and HMG-box DNA-binding protein 1
+分子 #15: Protein timeless homolog
+分子 #16: TIMELESS-interacting protein
+分子 #19: Leucine-rich repeat protein 1
+分子 #20: Elongin-B
+分子 #21: Claspin
+分子 #22: Elongin-C
+分子 #23: Cullin-2
+分子 #24: E3 ubiquitin-protein ligase RBX1
+分子 #17: Leading strand DNA
+分子 #18: Lagging strand DNA
+分子 #25: ZINC ION
+分子 #26: MAGNESIUM ION
+分子 #27: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+分子 #28: SULFATE 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 |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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: 16721 / 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 | C2レンズ絞り径: 2.7 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 0.1 mm 最大 デフォーカス(公称値): 2.8000000000000003 µm 最小 デフォーカス(公称値): 0.8 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |