+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25873 | ||||||||||||
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タイトル | Cryo-EM 3D map of the S. cerevisiae clamp-clamp loader complex PCNA-RFC bound to DNA with an open clamp | ||||||||||||
マップデータ | 3D cryoEM map of yeast RFC-PCNA-DNA1 complex in the open clamp state | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 DNA clamp unloader activity / DNA clamp unloading / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Ctf18 RFC-like complex / Rad17 RFC-like complex / DNA replication factor C complex ...DNA clamp unloader activity / DNA clamp unloading / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / Ctf18 RFC-like complex / Rad17 RFC-like complex / DNA replication factor C complex / Elg1 RFC-like complex / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / maintenance of DNA trinucleotide repeats / DNA clamp loader activity / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / DNA replication checkpoint signaling / PCNA complex / Activation of ATR in response to replication stress / Termination of translesion DNA synthesis / lagging strand elongation / postreplication repair / sister chromatid cohesion / silent mating-type cassette heterochromatin formation / mitotic sister chromatid cohesion / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / translesion synthesis / positive regulation of DNA repair / positive regulation of DNA replication / replication fork / DNA damage checkpoint signaling / nucleotide-excision repair / DNA-templated DNA replication / mitotic cell cycle / chromosome, telomeric region / cell division / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | synthetic construct (人工物) / Saccharomyces cerevisiae (パン酵母) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.41 Å | ||||||||||||
データ登録者 | Zheng F / Georgescu R / Yao YN / O'Donnell ME / Li H | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Elife / 年: 2022 タイトル: Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. 著者: Fengwei Zheng / Roxana Georgescu / Nina Y Yao / Huilin Li / Michael E O'Donnell / 要旨: RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during ...RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases δ and ε. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a second DNA binding site in RFC that binds a 5' duplex. This 5' DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3' and 5' ends are present at a ssDNA gap, we propose that the 5' site facilitates RFC's PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5' DNA binding domain of Rfc1. We further observe that a 5' end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5'-DNA site in lagging strand DNA synthesis. | ||||||||||||
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_25873.map.gz | 230.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25873-v30.xml emd-25873.xml | 22.5 KB 22.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25873.png | 59.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25873 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25873 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25873_validation.pdf.gz | 457.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25873_full_validation.pdf.gz | 457 KB | 表示 | |
XML形式データ | emd_25873_validation.xml.gz | 7.1 KB | 表示 | |
CIF形式データ | emd_25873_validation.cif.gz | 8.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25873 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25873 | 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_25873.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 | 3D cryoEM map of yeast RFC-PCNA-DNA1 complex in the open clamp state | ||||||||||||||||||||
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
-試料の構成要素
+全体 : RFC-PCNA-DNA1-DNA2
+超分子 #1: RFC-PCNA-DNA1-DNA2
+超分子 #2: dsDNA
+超分子 #3: Proteins
+分子 #1: Replication factor C subunit 1
+分子 #2: Replication factor C subunit 4
+分子 #3: Replication factor C subunit 3
+分子 #4: Replication factor C subunit 2
+分子 #5: Replication factor C subunit 5
+分子 #6: Proliferating cell nuclear antigen
+分子 #7: Template strand
+分子 #8: Primer strand
+分子 #9: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+分子 #10: MAGNESIUM ION
+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
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 (6k x 4k) / 平均電子線量: 65.0 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): 1.3 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.41 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 118384 |
初期 角度割当 | タイプ: NOT APPLICABLE |
最終 角度割当 | タイプ: NOT APPLICABLE |