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- EMDB-50222: Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) -
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データを開く
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基本情報
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タイトル | Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) | |||||||||
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![]() | DNA / polymerase / epsilon / PCNA / leading strand / human / replication / replisome / proofreading | |||||||||
機能・相同性 | ![]() DNA replication initiation / epsilon DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity ...DNA replication initiation / epsilon DNA polymerase complex / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / single-stranded DNA 3'-5' DNA exonuclease activity / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Activation of the pre-replicative complex / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / 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 / nucleotide-excision repair, DNA gap filling / response to L-glutamate / DNA replication proofreading / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / positive regulation of DNA replication / G1/S-Specific Transcription / replication fork processing / response to dexamethasone / leading strand elongation / nuclear replication fork / cyclin-dependent protein kinase holoenzyme complex / SUMOylation of DNA replication proteins / estrous cycle / epithelial cell differentiation / PCNA-Dependent Long Patch Base Excision Repair / positive regulation of DNA repair / embryonic organ development / mismatch repair / male germ cell nucleus / translesion synthesis / response to cadmium ion / DNA polymerase binding / liver regeneration / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / G1/S transition of mitotic cell cycle / Dual Incision in GG-NER / DNA-templated DNA replication / receptor tyrosine kinase binding / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to xenobiotic stimulus / cellular response to UV / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / mitotic cell cycle / heart development / 4 iron, 4 sulfur cluster binding / chromosome, telomeric region / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / chromatin binding / centrosome / nucleotide binding / chromatin / protein-containing complex binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / plasma membrane 類似検索 - 分子機能 | |||||||||
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手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | |||||||||
![]() | Roske JJ / Yeeles JTP | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis for processive daughter-strand synthesis and proofreading by the human leading-strand DNA polymerase Pol ε. 著者: Johann J Roske / Joseph T P Yeeles / ![]() 要旨: During chromosome replication, the nascent leading strand is synthesized by DNA polymerase epsilon (Pol ε), which associates with the sliding clamp processivity factor proliferating cell nuclear ...During chromosome replication, the nascent leading strand is synthesized by DNA polymerase epsilon (Pol ε), which associates with the sliding clamp processivity factor proliferating cell nuclear antigen (PCNA) to form a processive holoenzyme. For high-fidelity DNA synthesis, Pol ε relies on nucleotide selectivity and its proofreading ability to detect and excise a misincorporated nucleotide. Here, we present cryo-electron microscopy (cryo-EM) structures of human Pol ε in complex with PCNA, DNA and an incoming nucleotide, revealing how Pol ε associates with PCNA through its PCNA-interacting peptide box and additional unique features of its catalytic domain. Furthermore, by solving a series of cryo-EM structures of Pol ε at a mismatch-containing DNA, we elucidate how Pol ε senses and edits a misincorporated nucleotide. Our structures delineate steps along an intramolecular switching mechanism between polymerase and exonuclease activities, providing the basis for a proofreading mechanism in B-family replicative polymerases. | |||||||||
履歴 |
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構造の表示
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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 | ![]() | 223.6 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 21.9 KB 21.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.9 KB | 表示 | ![]() |
画像 | ![]() | 131.6 KB | ||
マスクデータ | ![]() ![]() | 236.9 MB 236.9 MB | ![]() | |
Filedesc metadata | ![]() | 7 KB | ||
その他 | ![]() ![]() ![]() | 223.6 MB 219.8 MB 219.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1 MB | 表示 | |
XML形式データ | ![]() | 21.3 KB | 表示 | |
CIF形式データ | ![]() | 26.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 9f6dMC ![]() 9f6eC ![]() 9f6fC ![]() 9f6iC ![]() 9f6jC ![]() 9f6kC ![]() 9f6lC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
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ボクセルのサイズ | X=Y=Z: 0.84065 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
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投影像・断面図 |
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密度ヒストグラム |
-マスク #2
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密度ヒストグラム |
-追加マップ: Map from focussed refinement with Mask around Polymerase...
ファイル | emd_50222_additional_1.map | ||||||||||||
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注釈 | Map from focussed refinement with Mask around Polymerase epsilon catalytic domain | ||||||||||||
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_50222_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_50222_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 |
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試料の構成要素
+全体 : Quaternary Complex of human leading strand polymerase epsilon, Pr...
+超分子 #1: Quaternary Complex of human leading strand polymerase epsilon, Pr...
+超分子 #2: DNA polymerase epsilon catalytic subunit A
+超分子 #3: Proliferating cell nuclear antigen
+超分子 #4: DNA
+分子 #1: DNA polymerase epsilon catalytic subunit A
+分子 #2: Proliferating cell nuclear antigen
+分子 #3: DNA nascent strand
+分子 #4: DNA template strand
+分子 #5: IRON/SULFUR CLUSTER
+分子 #6: 2',3'-dideoxyadenosine triphosphate
+分子 #7: MAGNESIUM 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
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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 BIOQUANTUM (6k x 4k) 平均電子線量: 40.08 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
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): 3.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |