+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-28001 | ||||||||||||
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タイトル | XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP) | ||||||||||||
マップデータ | |||||||||||||
試料 |
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キーワード | protein-DNA complex / DNA BINDING PROTEIN-DNA complex | ||||||||||||
機能・相同性 | 機能・相同性情報 nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / photoreceptor connecting cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / photoreceptor connecting cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / transcription export complex 2 / heterotrimeric G-protein binding / central nervous system myelin formation / response to auditory stimulus / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / UV protection / nuclear pore nuclear basket / embryonic cleavage / DNA 5'-3' helicase / G protein-coupled receptor internalization / UV-damage excision repair / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / intercellular bridge / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spinal cord development / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / erythrocyte maturation / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / centriole replication / ATPase activator activity / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / protein localization to nucleus / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / mRNA transport / embryonic organ development / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / SUMOylation of DNA damage response and repair proteins / Formation of RNA Pol II elongation complex / response to UV / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / RNA Polymerase II Pre-transcription Events / Anchoring of the basal body to the plasma membrane / DNA helicase activity / hormone-mediated signaling pathway / centriole / post-embryonic development / AURKA Activation by TPX2 / extracellular matrix organization / G-protein beta/gamma-subunit complex binding / insulin-like growth factor receptor signaling pathway / ciliary basal body / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of cytokinesis / determination of adult lifespan / isomerase activity / chromosome segregation / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription elongation by RNA polymerase II / DNA Damage Recognition in GG-NER 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (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: 3.6 Å | ||||||||||||
データ登録者 | Kim J / Yang W | ||||||||||||
資金援助 | 米国, 日本, 3件
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引用 | ジャーナル: Nature / 年: 2023 タイトル: Lesion recognition by XPC, TFIIH and XPA in DNA excision repair. 著者: Jinseok Kim / Chia-Lung Li / Xuemin Chen / Yanxiang Cui / Filip M Golebiowski / Huaibin Wang / Fumio Hanaoka / Kaoru Sugasawa / Wei Yang / 要旨: Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA ...Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification. | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_28001.map.gz | 95.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-28001-v30.xml emd-28001.xml | 36.7 KB 36.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_28001_fsc.xml | 10.7 KB | 表示 | FSCデータファイル |
画像 | emd_28001.png | 80.7 KB | ||
Filedesc metadata | emd-28001.cif.gz | 10.6 KB | ||
その他 | emd_28001_half_map_1.map.gz emd_28001_half_map_2.map.gz | 80.9 MB 81 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-28001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28001 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_28001_validation.pdf.gz | 715 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_28001_full_validation.pdf.gz | 714.5 KB | 表示 | |
XML形式データ | emd_28001_validation.xml.gz | 17.8 KB | 表示 | |
CIF形式データ | emd_28001_validation.cif.gz | 23.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28001 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28001 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ebxMC 8ebsC 8ebtC 8ebuC 8ebvC 8ebwC 8ebyC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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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
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_28001.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: #1
ファイル | emd_28001_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_28001_half_map_2.map | ||||||||||||
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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 : small DNA lesion recognition complex3
+超分子 #1: small DNA lesion recognition complex3
+分子 #1: TFIIH basal transcription factor complex helicase XPB subunit
+分子 #2: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #3: General transcription factor IIH subunit 1
+分子 #4: General transcription factor IIH subunit 4, p52
+分子 #5: General transcription factor IIH subunit 2
+分子 #6: General transcription factor IIH subunit 3
+分子 #7: General transcription factor IIH subunit 5
+分子 #8: Xeroderma pigmentosum, complementation group C, isoform CRA_a
+分子 #9: Centrin-2
+分子 #10: DNA repair protein complementing XP-A cells
+分子 #11: DNA (Ap)
+分子 #12: DNA
+分子 #13: IRON/SULFUR CLUSTER
+分子 #14: ZINC ION
+分子 #15: CALCIUM 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 | 0.4 mg/mL | ||||||||||||||||||
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緩衝液 | pH: 7.9 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. | ||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV |
-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) / 撮影したグリッド数: 1 / 実像数: 3883 / 平均露光時間: 2.5 sec. / 平均電子線量: 54.1 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |