+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8pbd | |||||||||
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タイトル | RAD51 filament on dsDNA bound by the BRCA2 c-terminus | |||||||||
要素 |
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キーワード | RECOMBINATION / RAD51 / BRCA2 / Filament / Complex | |||||||||
機能・相同性 | 機能・相同性情報 BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / establishment of protein localization to telomere / DNA recombinase assembly / telomere maintenance via telomere lengthening / Impaired BRCA2 translocation to the nucleus ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / presynaptic intermediate filament cytoskeleton / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / cellular response to camptothecin / establishment of protein localization to telomere / DNA recombinase assembly / telomere maintenance via telomere lengthening / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / positive regulation of DNA ligation / DNA strand invasion / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / mitotic recombination / cellular response to hydroxyurea / DNA strand exchange activity / lateral element / replication-born double-strand break repair via sister chromatid exchange / telomere maintenance via recombination / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / single-stranded DNA helicase activity / reciprocal meiotic recombination / response to UV-C / DNA repair complex / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / oocyte maturation / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / ATP-dependent DNA damage sensor activity / HDR through Single Strand Annealing (SSA) / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / regulation of double-strand break repair via homologous recombination / nuclear chromosome / female gonad development / DNA unwinding involved in DNA replication / replication fork processing / male meiosis I / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / response to gamma radiation / condensed nuclear chromosome / male germ cell nucleus / meiotic cell cycle / nucleotide-excision repair / cellular response to ionizing radiation / brain development / regulation of protein phosphorylation / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / PML body / Meiotic recombination / cellular senescence / double-strand break repair / single-stranded DNA binding / site of double-strand break / double-stranded DNA binding / spermatogenesis / protease binding / DNA recombination / chromosome, telomeric region / mitochondrial matrix / DNA repair / centrosome / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / enzyme binding / ATP hydrolysis activity / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) synthetic construct (人工物) | |||||||||
手法 | 電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 2.83 Å | |||||||||
データ登録者 | Appleby, R. / Pellegrini, L. | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Structural basis for stabilisation of the RAD51 nucleoprotein filament by BRCA2. 著者: Robert Appleby / Luay Joudeh / Katie Cobbett / Luca Pellegrini / 要旨: The BRCA2 tumour suppressor protein preserves genomic integrity via interactions with the DNA-strand exchange RAD51 protein in homology-directed repair. The RAD51-binding TR2 motif at the BRCA2 C- ...The BRCA2 tumour suppressor protein preserves genomic integrity via interactions with the DNA-strand exchange RAD51 protein in homology-directed repair. The RAD51-binding TR2 motif at the BRCA2 C-terminus is essential for protection and restart of stalled replication forks. Biochemical evidence shows that TR2 recognises filamentous RAD51, but existing models of TR2 binding to RAD51 lack a structural basis. Here we used cryo-electron microscopy and structure-guided mutagenesis to elucidate the mechanism of TR2 binding to nucleoprotein filaments of human RAD51. We find that TR2 binds across the protomer interface in the filament, acting as a brace for adjacent RAD51 molecules. TR2 targets an acidic-patch motif on human RAD51 that serves as a recruitment hub in fission yeast Rad51 for recombination mediators Rad52 and Rad55-Rad57. Our findings provide a structural rationale for RAD51 filament stabilisation by BRCA2 and reveal a common recruitment mechanism of recombination mediators to the RAD51 filament. | |||||||||
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 | 8pbd.cif.gz | 647.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8pbd.ent.gz | 529.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8pbd.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 | 8pbd_validation.pdf.gz | 1.8 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8pbd_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 8pbd_validation.xml.gz | 88.6 KB | 表示 | |
CIF形式データ | 8pbd_validation.cif.gz | 115 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pbd ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pbd | HTTPS FTP |
-関連構造データ
関連構造データ | 17585MC 8pbcC M: このデータのモデリングに利用したマップデータ 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
-集合体
登録構造単位 |
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1 |
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-要素
-DNA鎖 , 2種, 2分子 TU
#3: DNA鎖 | 分子量: 8699.608 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
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#4: DNA鎖 | 分子量: 7898.048 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-タンパク質 / タンパク質・ペプチド , 2種, 19分子 ABCDEFGHIJKLMNOPQRS
#1: タンパク質 | 分子量: 37009.125 Da / 分子数: 10 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RAD51, RAD51A, RECA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q06609 #2: タンパク質・ペプチド | 分子量: 5483.415 Da / 分子数: 9 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P51587 |
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-非ポリマー , 2種, 30分子
#5: 化合物 | ChemComp-ATP / #6: 化合物 | ChemComp-CA / |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 |
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分子量 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.4 | |||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | |||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 130000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 900 nm |
試料ホルダ | 凍結剤: NITROGEN |
撮影 | 電子線照射量: 52.6 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
らせん対称 | 回転角度/サブユニット: 56 ° / 軸方向距離/サブユニット: 15.8 Å / らせん対称軸の対称性: C1 | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.83 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 1 / 対称性のタイプ: HELICAL | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL |