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基本情報
登録情報 | データベース: PDB / ID: 7kc0 | ||||||||||||
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タイトル | Structure of the Saccharomyces cerevisiae replicative polymerase delta in complex with a primer/template and the PCNA clamp | ||||||||||||
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![]() | REPLICATION / Polymerase delta / PCNA / primed DNA / complex | ||||||||||||
機能・相同性 | ![]() delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / zeta DNA polymerase complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / RNA-templated DNA biosynthetic process / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins ...delta DNA polymerase complex / DNA-templated DNA replication maintenance of fidelity / DNA amplification / zeta DNA polymerase complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / RNA-templated DNA biosynthetic process / meiotic mismatch repair / Processive synthesis on the lagging strand / Removal of the Flap Intermediate / E3 ubiquitin ligases ubiquitinate target proteins / Polymerase switching / SUMOylation of DNA replication proteins / positive regulation of DNA metabolic process / DNA replication, removal of RNA primer / maintenance of DNA trinucleotide repeats / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / establishment of mitotic sister chromatid cohesion / PCNA complex / Termination of translesion DNA synthesis / lagging strand elongation / double-strand break repair via break-induced replication / postreplication repair / silent mating-type cassette heterochromatin formation / 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 / 3'-5'-DNA exonuclease activity / DNA metabolic process / mitotic sister chromatid cohesion / DNA replication proofreading / DNA strand elongation involved in DNA replication / error-free translesion synthesis / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / Dual incision in TC-NER / subtelomeric heterochromatin formation / mismatch repair / error-prone translesion synthesis / translesion synthesis / positive regulation of DNA repair / base-excision repair, gap-filling / positive regulation of DNA replication / replication fork / nucleotide-excision repair / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / DNA replication / chromosome, telomeric region / molecular adaptor activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / identical protein binding / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() ![]() | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | ||||||||||||
![]() | Zheng, F. / Georgescu, R. / Li, H. / O'Donnell, M.E. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structure of eukaryotic DNA polymerase δ bound to the PCNA clamp while encircling DNA. 著者: Fengwei Zheng / Roxana E Georgescu / Huilin Li / Michael E O'Donnell / ![]() 要旨: The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and ...The DNA polymerase (Pol) δ of (S.c.) is composed of the catalytic subunit Pol3 along with two regulatory subunits, Pol31 and Pol32. Pol δ binds to proliferating cell nuclear antigen (PCNA) and functions in genome replication, repair, and recombination. Unique among DNA polymerases, the Pol3 catalytic subunit contains a 4Fe-4S cluster that may sense the cellular redox state. Here we report the 3.2-Å cryo-EM structure of S.c. Pol δ in complex with primed DNA, an incoming ddTTP, and the PCNA clamp. Unexpectedly, Pol δ binds only one subunit of the PCNA trimer. This singular yet extensive interaction holds DNA such that the 2-nm-wide DNA threads through the center of the 3-nm interior channel of the clamp without directly contacting the protein. Thus, a water-mediated clamp and DNA interface enables the PCNA clamp to "waterskate" along the duplex with minimum drag. Pol31 and Pol32 are positioned off to the side of the catalytic Pol3-PCNA-DNA axis. We show here that Pol31-Pol32 binds single-stranded DNA that we propose underlies polymerase recycling during lagging strand synthesis, in analogy to replicase. Interestingly, the 4Fe-4S cluster in the C-terminal CysB domain of Pol3 forms the central interface to Pol31-Pol32, and this strategic location may explain the regulation of the oxidation state on Pol δ activity, possibly useful during cellular oxidative stress. Importantly, human cancer and other disease mutations map to nearly every domain of Pol3, suggesting that all aspects of Pol δ replication are important to human health and disease. | ||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 444.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 360.7 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
-DNA鎖 , 2種, 2分子 PT
#1: DNA鎖 | 分子量: 7681.985 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) ![]() ![]() |
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#2: DNA鎖 | 分子量: 11677.539 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) ![]() ![]() |
-タンパク質 , 4種, 6分子 FEGABC
#3: タンパク質 | 分子量: 28944.051 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: PCNA, POL30, GI526_G0000296, PACBIOSEQ_LOCUS349, PACBIOSEQ_LOCUS352, PACBIOSEQ_LOCUS359, PACBIOSEQ_LOCUS364, PACBIOSEQ_LOCUS365, PACBIOSEQ_LOCUS366, PACBIOSEQ_LOCUS371 発現宿主: ![]() ![]() #4: タンパク質 | | 分子量: 124707.359 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: POL3, GI526_G0000818 / 発現宿主: ![]() ![]() 参照: UniProt: A0A6A5Q0V0, UniProt: P15436*PLUS, DNA-directed DNA polymerase #5: タンパク質 | | 分子量: 55352.688 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: POL31, GI526_G0003241 / 発現宿主: ![]() ![]() #6: タンパク質 | | 分子量: 40377.715 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: POL32, GI526_G0003272, PACBIOSEQ_LOCUS3556, PACBIOSEQ_LOCUS3579 発現宿主: ![]() ![]() |
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-非ポリマー , 4種, 5分子 ![](data/chem/img/MG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/D3T.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/D3T.gif)
![](data/chem/img/ZN.gif)
#7: 化合物 | #8: 化合物 | ChemComp-SF4 / | #9: 化合物 | ChemComp-D3T / | #10: 化合物 | ChemComp-ZN / | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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由来(天然) |
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由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 68 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
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解析
ソフトウェア | 名称: PHENIX / バージョン: 1.17.1_3660: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 133468 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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