+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23089 | |||||||||
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タイトル | Structure of the human fanconi anaemia Core-UBE2T-ID-DNA complex in intermediate state | |||||||||
マップデータ | composite REFMAC5 map (masked) used in coordinate refinement | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / homologous chromosome pairing at meiosis / gamete generation ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / protein K29-linked ubiquitination / protein K27-linked ubiquitination / regulation of regulatory T cell differentiation / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / homologous chromosome pairing at meiosis / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance / protein K6-linked ubiquitination / protein K11-linked ubiquitination / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / myeloid cell homeostasis / E2 ubiquitin-conjugating enzyme / female gonad development / protein monoubiquitination / germ cell development / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / spermatid development / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / DNA polymerase binding / ovarian follicle development / condensed chromosome / removal of superoxide radicals / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / mitochondrion organization / nucleotide-excision repair / Fanconi Anemia Pathway / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / RING-type E3 ubiquitin transferase / response to radiation / PKR-mediated signaling / protein polyubiquitination / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / nuclear envelope / chromosome / regulation of cell population proliferation / cellular response to oxidative stress / regulation of inflammatory response / protein-containing complex assembly / damaged DNA binding / nuclear body / intracellular membrane-bounded organelle / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / human (ヒト) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.2 Å | |||||||||
データ登録者 | Wang SL / Pavletich NP | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2021 タイトル: Structure of the FA core ubiquitin ligase closing the ID clamp on DNA. 著者: Shengliu Wang / Renjing Wang / Christopher Peralta / Ayat Yaseen / Nikola P Pavletich / 要旨: The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates ...The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates the FANCI-FANCD2 (ID) DNA clamp. The 3.1 Å structure of the 1.1-MDa human FA core complex, described here, reveals an asymmetric assembly with two copies of all but the FANCC, FANCE and FANCF subunits. The asymmetry is crucial, as it prevents the binding of a second FANCC-FANCE-FANCF subcomplex that inhibits the recruitment of the UBE2T ubiquitin conjugating enzyme, and instead creates an ID binding site. A single active site then ubiquitinates FANCD2 and FANCI sequentially. We also present the 4.2-Å structures of the human core-UBE2T-ID-DNA complex in three conformations captured during monoubiquitination. They reveal the core-UBE2T complex remodeling the ID-DNA complex, closing the clamp on the DNA before ubiquitination. Monoubiquitination then prevents clamp opening after release from the core. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_23089.map.gz | 60 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23089-v30.xml emd-23089.xml | 42.2 KB 42.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_23089.png | 64.4 KB | ||
その他 | emd_23089_additional_1.map.gz emd_23089_additional_2.map.gz emd_23089_additional_3.map.gz emd_23089_additional_4.map.gz emd_23089_additional_5.map.gz | 20.7 MB 17.1 MB 19.7 MB 16.9 MB 16 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23089 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23089 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23089_validation.pdf.gz | 310.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23089_full_validation.pdf.gz | 310.3 KB | 表示 | |
XML形式データ | emd_23089_validation.xml.gz | 7.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23089 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23089 | 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_23089.map.gz / 形式: CCP4 / 大きさ: 343 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | composite REFMAC5 map (masked) used in coordinate refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: consensus reconstruction postprocessed with relion
ファイル | emd_23089_additional_1.map | ||||||||||||
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注釈 | consensus reconstruction postprocessed with relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focus1: reconstruction (masked) focused at FANCC-Entd-F-L-G and FANCB-FAAP100...
ファイル | emd_23089_additional_2.map | ||||||||||||
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注釈 | focus1: reconstruction (masked) focused at FANCC-Entd-F-L-G and FANCB-FAAP100 WD40 domains postprocessed with relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focus2: reconstruction (masked) focused at FANCA' NTD, FANCG'-Ectd-L',...
ファイル | emd_23089_additional_3.map | ||||||||||||
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注釈 | focus2: reconstruction (masked) focused at FANCA' NTD, FANCG'-Ectd-L', FANCB-FAAP100 dimer of heterodimers, the ID-DNA complex and UBE2T postprocessed with relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focus3: reconstruction (masked) focused at FANCA-A' dimer and...
ファイル | emd_23089_additional_4.map | ||||||||||||
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注釈 | focus3: reconstruction (masked) focused at FANCA-A' dimer and FANCG' postprocessed with relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focus4: reconstruction (masked) focused at FANCEctd-FANCL', the ID-DNA...
ファイル | emd_23089_additional_5.map | ||||||||||||
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注釈 | focus4: reconstruction (masked) focused at FANCEctd-FANCL', the ID-DNA complex and UBE2T postprocessed with relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Human Fanconi Anaemia Core-UBE2T-ID-DNA complex
+超分子 #1: Human Fanconi Anaemia Core-UBE2T-ID-DNA complex
+分子 #1: Fanconi anemia group A protein
+分子 #2: Fanconi anemia group B protein
+分子 #3: Fanconi anemia group C protein
+分子 #4: Fanconi anemia group E protein
+分子 #5: Fanconi anemia group F protein
+分子 #6: Fanconi anemia group G protein
+分子 #7: E3 ubiquitin-protein ligase FANCL
+分子 #8: Fanconi anemia core complex-associated protein 100
+分子 #9: Fanconi anemia core complex-associated protein 20
+分子 #10: Ubiquitin-conjugating enzyme E2 T
+分子 #11: Fanconi anemia, complementation group I
+分子 #12: Fanconi anemia group D2 protein
+分子 #13: DNA (22-MER)
+分子 #14: DNA (22-MER)
+分子 #15: ZINC ION
-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
濃度 | 1 mg/mL | |||||||||||||||
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緩衝液 | pH: 8 構成要素:
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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) / 検出モード: SUPER-RESOLUTION / 平均電子線量: 36.5 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 69111 |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |