+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-42388 | |||||||||
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タイトル | Cryo-EM map of the human CTF18-RFC-PCNA-DNA ternary complex with narrow PCNA opening state II (state 6) | |||||||||
マップデータ | EM sharpen map | |||||||||
試料 |
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キーワード | DNA clamp loader complex / REPLICATION-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / response to organophosphorus / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / Elg1 RFC-like complex / Ctf18 RFC-like complex / DNA replication factor C complex / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity ...positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / response to organophosphorus / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / Elg1 RFC-like complex / Ctf18 RFC-like complex / DNA replication factor C complex / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of DNA-directed DNA polymerase activity / MutLalpha complex binding / nuclear lamina / DNA clamp loader activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / Transcription of E2F targets under negative control by DREAM complex / replisome / response to L-glutamate / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA strand elongation involved in DNA replication / histone acetyltransferase binding / DNA synthesis involved in DNA repair / leading strand elongation / DNA polymerase processivity factor activity / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / estrous cycle / mismatch repair / translesion synthesis / ATP-dependent activity, acting on DNA / Activation of ATR in response to replication stress / response to cadmium ion / DNA polymerase binding / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by POLK / 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 / nuclear estrogen receptor binding / liver regeneration / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / G2/M DNA damage checkpoint / 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 / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / centrosome / chromatin binding / protein-containing complex binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / ATP hydrolysis activity / DNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol 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: 2.83 Å | |||||||||
データ登録者 | Wang F / He Q / Li H | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2024 タイトル: Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC. 著者: Qing He / Feng Wang / Michael E O'Donnell / Huilin Li / 要旨: The DNA sliding clamp PCNA is a multipurpose platform for DNA polymerases and many other proteins involved in DNA metabolism. The topologically closed PCNA ring needs to be cracked open and loaded ...The DNA sliding clamp PCNA is a multipurpose platform for DNA polymerases and many other proteins involved in DNA metabolism. The topologically closed PCNA ring needs to be cracked open and loaded onto DNA by a clamp loader, e.g., the well-studied pentameric ATPase complex RFC (RFC1-5). The CTF18-RFC complex is an alternative clamp loader found recently to bind the leading strand DNA polymerase ε and load PCNA onto leading strand DNA, but its structure and the loading mechanism have been unknown. By cryo-EM analysis of in vitro assembled human CTF18-RFC-DNA-PCNA complex, we have captured seven loading intermediates, revealing a detailed PCNA loading mechanism onto a 3'-ss/dsDNA junction by CTF18-RFC. Interestingly, the alternative loader has evolved a highly mobile CTF18 AAA+ module likely to lower the loading activity, perhaps to avoid competition with the RFC and to limit its role to leading strand clamp loading. To compensate for the lost stability due to the mobile AAA+ module, CTF18 has evolved a unique β-hairpin motif that reaches across RFC2 to interact with RFC5, thereby stabilizing the pentameric complex. Further, we found that CTF18 also contains a separation pin to locally melt DNA from the 3'-end of the primer; this ensures its ability to load PCNA to any 3'-ss/dsDNA junction, facilitated by the binding energy of the E-plug to the major groove. Our study reveals unique structural features of the human CTF18-RFC and contributes to a broader understanding of PCNA loading by the alternative clamp loaders. | |||||||||
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_42388.map.gz | 117.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-42388-v30.xml emd-42388.xml | 28.7 KB 28.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_42388_fsc.xml | 10.6 KB | 表示 | FSCデータファイル |
画像 | emd_42388.png | 61.6 KB | ||
Filedesc metadata | emd-42388.cif.gz | 8.1 KB | ||
その他 | emd_42388_additional_1.map.gz emd_42388_additional_2.map.gz emd_42388_half_map_1.map.gz emd_42388_half_map_2.map.gz | 110.8 MB 62.6 MB 116.1 MB 116.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-42388 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42388 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_42388_validation.pdf.gz | 953.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_42388_full_validation.pdf.gz | 953.5 KB | 表示 | |
XML形式データ | emd_42388_validation.xml.gz | 18.9 KB | 表示 | |
CIF形式データ | emd_42388_validation.cif.gz | 24.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42388 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42388 | HTTPS FTP |
-関連構造データ
関連構造データ | 8umyMC 8umtC 8umuC 8umvC 8umwC 8un0C 8unjC 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_42388.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | EM sharpen map | ||||||||||||||||||||||||||||||||||||
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: 0.828 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
-追加マップ: EM sharpen map by DeepEMhancer
ファイル | emd_42388_additional_1.map | ||||||||||||
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注釈 | EM sharpen map by DeepEMhancer | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Original unsharpen EM map
ファイル | emd_42388_additional_2.map | ||||||||||||
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注釈 | Original unsharpen EM map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: EM half map A
ファイル | emd_42388_half_map_1.map | ||||||||||||
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注釈 | EM half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: EM half map B
ファイル | emd_42388_half_map_2.map | ||||||||||||
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注釈 | EM half map B | ||||||||||||
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 : the human clamp-clamp loader complex PCNA-CTF18
+超分子 #1: the human clamp-clamp loader complex PCNA-CTF18
+分子 #1: Chromosome transmission fidelity protein 18 homolog
+分子 #2: Replication factor C subunit 2
+分子 #3: Replication factor C subunit 5
+分子 #4: Replication factor C subunit 4
+分子 #5: Replication factor C subunit 3
+分子 #6: Proliferating cell nuclear antigen
+分子 #7: DNA (40-MER)
+分子 #8: DNA (20-MER)
+分子 #9: MAGNESIUM ION
+分子 #10: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+分子 #11: ADENOSINE-5'-DIPHOSPHATE
-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
濃度 | 0.3 mg/mL |
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緩衝液 | pH: 7.5 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 280 K / 装置: FEI VITROBOT MARK IV |
-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 (6k x 4k) / 平均電子線量: 60.0 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): 1.9000000000000001 µm 最小 デフォーカス(公称値): 1.2 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 温度因子: 123 |
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得られたモデル | PDB-8umy: |