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万見- EMDB-50222: Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-50222 | |||||||||
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タイトル | Human DNA polymerase epsilon bound to DNA and PCNA (open conformation) | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | DNA / polymerase / epsilon / PCNA / leading strand / human / replication / replisome / proofreading | |||||||||
機能・相同性 | 機能・相同性情報 DNA replication initiation / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / epsilon DNA polymerase complex / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity ...DNA replication initiation / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / epsilon DNA polymerase complex / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / MutLalpha complex binding / nuclear lamina / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / nucleotide-excision repair, DNA gap filling / single-stranded DNA 3'-5' DNA exonuclease activity / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Polymerase switching on the C-strand of the telomere / DNA replication proofreading / 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 / response to L-glutamate / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / replication fork processing / response to dexamethasone / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / mismatch repair / embryonic organ development / translesion synthesis / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / epithelial cell differentiation / base-excision repair, gap-filling / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / male germ cell nucleus / replication fork / liver regeneration / 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) / Dual Incision in GG-NER / receptor tyrosine kinase binding / DNA-templated DNA replication / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / G1/S transition of mitotic cell cycle / cellular response to UV / cellular response to xenobiotic stimulus / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / heart development / 4 iron, 4 sulfur cluster binding / DNA replication / damaged DNA binding / chromosome, telomeric region / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear body / nucleotide binding / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / 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: 3.6 Å | |||||||||
データ登録者 | Roske JJ / Yeeles JTP | |||||||||
資金援助 | 英国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 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
添付画像 |
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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 | emd_50222.map.gz | 223.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-50222-v30.xml emd-50222.xml | 21.9 KB 21.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_50222_fsc.xml | 14.9 KB | 表示 | FSCデータファイル |
画像 | emd_50222.png | 131.6 KB | ||
マスクデータ | emd_50222_msk_1.map emd_50222_msk_2.map | 236.9 MB 236.9 MB | マスクマップ | |
Filedesc metadata | emd-50222.cif.gz | 7 KB | ||
その他 | emd_50222_additional_1.map.gz emd_50222_half_map_1.map.gz emd_50222_half_map_2.map.gz | 223.6 MB 219.8 MB 219.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-50222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50222 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_50222_validation.pdf.gz | 1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_50222_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | emd_50222_validation.xml.gz | 21.3 KB | 表示 | |
CIF形式データ | emd_50222_validation.cif.gz | 26.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50222 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50222 | 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 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_50222.map.gz / 形式: CCP4 / 大きさ: 236.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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: 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
ファイル | emd_50222_msk_1.map | ||||||||||||
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密度ヒストグラム |
-マスク #2
ファイル | emd_50222_msk_2.map | ||||||||||||
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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 |
-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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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: 7.5 |
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凍結 | 凍結剤: ETHANE |
-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: 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): 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 |