+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 / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / Unwinding of DNA / cell cycle phase transition / cellular response to cisplatin / DNA replication initiation ...cellular response to bleomycin / DNA secondary structure binding / detection of abiotic stimulus / replication fork arrest / regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / Unwinding of DNA / cell cycle phase transition / cellular response to cisplatin / DNA replication initiation / epsilon DNA polymerase complex / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / nuclear origin of replication recognition complex / cellular response to hydroxyurea / anaphase-promoting complex binding / cullin-RING-type E3 NEDD8 transferase / alpha DNA polymerase:primase complex / mitotic DNA replication / cellular response to chemical stress / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / CMG complex / DNA replication checkpoint signaling / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication preinitiation complex / target-directed miRNA degradation / MCM complex / regulation of phosphorylation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / replication fork protection complex / elongin complex / DNA replication proofreading / VCB complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / positive regulation of protein autoubiquitination / protein neddylation / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / mitotic intra-S DNA damage checkpoint signaling / NEDD8 ligase activity / Cul5-RING ubiquitin ligase complex / positive regulation of double-strand break repair / negative regulation of response to oxidative stress / DNA strand elongation involved in DNA replication / 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 / inner cell mass cell proliferation / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4B-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / activation of protein kinase activity / branching morphogenesis of an epithelial tube / DNA synthesis involved in DNA repair / cochlea development / G1/S-Specific Transcription / leading strand elongation / DNA unwinding involved in DNA replication / Apoptotic cleavage of cellular proteins / Prolactin receptor signaling / replication fork processing / nuclear replication fork / protein monoubiquitination / mitotic G2 DNA damage checkpoint signaling / 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 / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / DNA replication initiation / Tat-mediated elongation of the HIV-1 transcript / error-prone translesion synthesis / embryonic organ development / Formation of HIV-1 elongation complex containing HIV-1 Tat / cellular response to interleukin-4 / Formation of HIV elongation complex in the absence of HIV Tat / protein K48-linked ubiquitination / Activation of ATR in response to replication stress / RNA Polymerase II Transcription Elongation / Nuclear events stimulated by ALK signaling in cancer / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / base-excision repair, gap-filling / DNA helicase activity / positive regulation of TORC1 signaling 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.072 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 |