+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3ja9 | ||||||
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タイトル | Structure of native human PCNA | ||||||
要素 | Proliferating cell nuclear antigen | ||||||
キーワード | DNA BINDING PROTEIN / DNA / REPLICATION / PROCESSIVITY / ONCOGENE / DNA-BINDING SYSTEMIC LUPUS ERYTHEMATOSUS | ||||||
機能・相同性 | 機能・相同性情報 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 ...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 / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / 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 / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / mismatch repair / translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / response to cadmium ion / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of DNA replication / replication fork / male germ cell nucleus / 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 / 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 / chromosome, telomeric region / damaged DNA binding / nuclear body / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / nucleus 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / ネガティブ染色法 / 解像度: 22 Å | ||||||
データ登録者 | Lau, W.C.Y. / Li, Y. / Zhang, Q. / Huen, M.S.Y. | ||||||
引用 | ジャーナル: Sci Rep / 年: 2015 タイトル: Molecular architecture of the Ub-PCNA/Pol η complex bound to DNA. 著者: Wilson C Y Lau / Yinyin Li / Qinfen Zhang / Michael S Y Huen / 要旨: Translesion synthesis (TLS) is the mechanism by which DNA polymerases replicate through unrepaired DNA lesions. TLS is activated by monoubiquitination of the homotrimeric proliferating cell nuclear ...Translesion synthesis (TLS) is the mechanism by which DNA polymerases replicate through unrepaired DNA lesions. TLS is activated by monoubiquitination of the homotrimeric proliferating cell nuclear antigen (PCNA) at lysine-164, followed by the switch from replicative to specialized polymerases at DNA damage sites. Pol η belongs to the Y-Family of specialized polymerases that can efficiently bypass UV-induced lesions. Like other members of the Y-Family polymerases, its recruitment to the damaged sites is mediated by the interaction with monoubiquitinated PCNA (Ub-PCNA) via its ubiquitin-binding domain and non-canonical PCNA-interacting motif in the C-terminal region. The structural determinants underlying the direct recognition of Ub-PCNA by Pol η, or Y-Family polymerases in general, remain largely unknown. Here we report a structure of the Ub-PCNA/Pol η complex bound to DNA determined by single-particle electron microscopy (EM). The overall obtained structure resembles that of the editing PCNA/PolB complex. Analysis of the map revealed the conformation of ubiquitin that binds the C-terminal domain of Pol η. Our present study suggests that the Ub-PCNA/Pol η interaction requires the formation of a structured binding interface, which is dictated by the inherent flexibility of Ub-PCNA. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3ja9.cif.gz | 153.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3ja9.ent.gz | 126.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3ja9.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 3ja9_validation.pdf.gz | 689.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3ja9_full_validation.pdf.gz | 714.4 KB | 表示 | |
XML形式データ | 3ja9_validation.xml.gz | 28.2 KB | 表示 | |
CIF形式データ | 3ja9_validation.cif.gz | 42.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ja/3ja9 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3ja9 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 28795.752 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PCNA / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P12004 #2: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 / 使用した結晶の数: 1 |
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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 |
-試料調製
構成要素 | 名称: Ub-PCNA/Pol eta/DNA / タイプ: COMPLEX 詳細: Monomeric catalytic core of Pol eta binds to one homotrimeric Ub-PCNA 別称: Monoubiquitinated PCNA |
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分子量 | 値: 0.2 MDa / 実験値: YES |
緩衝液 | pH: 8 / 詳細: 50mM Tris-HCl, 5mM MgCl2 |
試料 | 包埋: NO / シャドウイング: NO / 染色: YES / 凍結: NO 詳細: 50mM Tris-HCl, 5mM MgCl2 (Stain Details Grids with adsorbed protein floated on two 20 ul drops of 2% w/v uranyl acetate solution for 30 seconds) |
染色 | タイプ: NEGATIVE / 染色剤: Uranyl Acetate |
試料支持 | 詳細: Continuous carbon coated copper grids (Ted Pella), glow-discharged for 30 seconds |
-電子顕微鏡撮影
顕微鏡 | モデル: JEOL 2010 / 日付: 2014年11月12日 |
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電子銃 | 電子線源: LAB6 / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 18 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Particles | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 手法: Projection matching / 解像度: 22 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 7330 / 詳細: (Single particle--Applied symmetry: C1) / クラス平均像の数: 227 / 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / 詳細: REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
原子モデル構築 | PDB-ID: 1VYM | ||||||||||||
精密化ステップ | サイクル: LAST
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