+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ui9 | ||||||||||||
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タイトル | Cryo-EM map of human clamp-clamp loader ATAD5-RFC-cracked PCNA complex in intermediate state 2 | ||||||||||||
要素 |
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キーワード | MOTOR PROTEIN / AAA ATPase / Clamp unloader | ||||||||||||
機能・相同性 | 機能・相同性情報 DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / response to organophosphorus / Ctf18 RFC-like complex / DNA clamp loader activity / nuclear DNA replication / DNA replication factor C complex ...DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / response to organophosphorus / Ctf18 RFC-like complex / DNA clamp loader activity / nuclear DNA replication / DNA replication factor C complex / Elg1 RFC-like complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of isotype switching to IgG isotypes / 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 / isotype switching / 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 / Activation of ATR in response to replication stress / regulation of mitotic cell cycle phase transition / DNA duplex unwinding / response to L-glutamate / 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 / DNA polymerase processivity factor activity / positive regulation of DNA replication / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / G1/S-Specific Transcription / replication fork processing / response to dexamethasone / leading strand elongation / nuclear replication fork / cyclin-dependent protein kinase holoenzyme complex / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of DNA replication proteins / estrous cycle / epithelial cell differentiation / PCNA-Dependent Long Patch Base Excision Repair / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA repair / signal transduction in response to DNA damage / ATP-dependent activity, acting on DNA / mismatch repair / male germ cell nucleus / translesion synthesis / response to cadmium ion / DNA polymerase binding / positive regulation of B cell proliferation / liver regeneration / Translesion synthesis by REV1 / Translesion synthesis by POLK / base-excision repair, gap-filling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / G2/M DNA damage checkpoint / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / 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 xenobiotic stimulus / cellular response to UV / Processing of DNA double-strand break ends / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / chromosome, telomeric region / DNA replication / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / damaged DNA binding / nuclear body / DNA repair / chromatin binding / centrosome / chromatin / protein-containing complex binding 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 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | ||||||||||||
データ登録者 | Wang, F. / He, Q. / Li, H. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. 著者: Feng Wang / Qing He / Nina Y Yao / Michael E O'Donnell / Huilin Li / 要旨: Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying ...Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8ui9.cif.gz | 559.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ui9.ent.gz | 442.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8ui9.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 | 8ui9_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8ui9_full_validation.pdf.gz | 1.7 MB | 表示 | |
XML形式データ | 8ui9_validation.xml.gz | 87.3 KB | 表示 | |
CIF形式データ | 8ui9_validation.cif.gz | 128.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ui/8ui9 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/8ui9 | 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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1 |
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-要素
-タンパク質 , 2種, 4分子 AFGH
#1: タンパク質 | 分子量: 116421.094 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ATAD5 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: Q96QE3 |
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#6: 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: Insect cell expression vector pTIE1 (その他) 参照: UniProt: P12004 |
-Replication factor C subunit ... , 4種, 4分子 BCDE
#2: タンパク質 | 分子量: 39203.207 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RFC2 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: P35250 |
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#3: タンパク質 | 分子量: 38545.512 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RFC5 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: P40937 |
#4: タンパク質 | 分子量: 39735.711 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RFC4 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: P35249 |
#5: タンパク質 | 分子量: 40614.332 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RFC3 発現宿主: Insect cell expression vector pTIE1 (その他) 参照: UniProt: P40938 |
-非ポリマー , 3種, 9分子
#7: 化合物 | ChemComp-MG / #8: 化合物 | ChemComp-AGS / #9: 化合物 | ChemComp-ADP / | |
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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 |
-試料調製
構成要素 | 名称: ATAD5-RFC-cracked PCNA / タイプ: COMPLEX / Entity ID: #1-#6 / 由来: RECOMBINANT |
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分子量 | 値: 0.32 MDa / 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Insect cell expression vector pTIE1 (その他) |
緩衝液 | pH: 7.5 |
試料 | 濃度: 1 mg/ml / 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 |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI TITAN |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: DIFFRACTION / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 60 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 112347 / 対称性のタイプ: POINT |