+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-27997 | ||||||||||||
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タイトル | XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (Cy5) | ||||||||||||
マップデータ | |||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / positive regulation of DNA helicase activity ...nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / XPC complex / nucleotide-excision repair, DNA damage recognition / 9+2 motile cilium / MMXD complex / core TFIIH complex portion of holo TFIIH complex / photoreceptor connecting cilium / heterotrimeric G-protein binding / positive regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / transcription export complex 2 / response to auditory stimulus / central nervous system myelin formation / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / nucleotide-excision repair, preincision complex assembly / nuclear pore nuclear basket / 紫外線 / CAK-ERCC2 complex / embryonic cleavage / 5'-3' DNA helicase activity / G protein-coupled receptor internalization / UV-damage excision repair / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / 転写開始前複合体 / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / spinal cord development / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / 細胞結合 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / bone mineralization / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / ATPase activator activity / RNA Polymerase I Transcription Initiation / transcription elongation by RNA polymerase I / centriole replication / intrinsic apoptotic signaling pathway by p53 class mediator / protein localization to nucleus / transcription-coupled nucleotide-excision repair / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / embryonic organ development / mRNA transport / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / SUMOylation of DNA damage response and repair proteins / RNA Polymerase II Transcription Elongation / response to UV / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / 中心小体 / DNA helicase activity / hormone-mediated signaling pathway / extracellular matrix organization / AURKA Activation by TPX2 / post-embryonic development / insulin-like growth factor receptor signaling pathway / ciliary basal body / regulation of cytokinesis / chromosome segregation / determination of adult lifespan / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / DNA Damage Recognition in GG-NER / multicellular organism growth / G-protein beta/gamma-subunit complex binding / 塩基除去修復 / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / spindle 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: 3.9 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_27997.map.gz | 13.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-27997-v30.xml emd-27997.xml | 34.5 KB 34.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_27997_fsc.xml | 13.7 KB | 表示 | FSCデータファイル |
画像 | emd_27997.png | 93.7 KB | ||
その他 | emd_27997_half_map_1.map.gz emd_27997_half_map_2.map.gz | 152.1 MB 152.1 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-27997 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27997 | HTTPS FTP |
-関連構造データ
関連構造データ | 8ebtMC 8ebsC 8ebuC 8ebvC 8ebwC 8ebxC 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_27997.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.833 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_27997_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_27997_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 : protein DNA complex
+超分子 #1: protein DNA complex
+分子 #1: General transcription and DNA repair factor IIH helicase subunit XPB
+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
+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: DNA repair protein complementing XP-C cells
+分子 #9: Centrin-2
+分子 #10: DNA repair protein complementing XP-A cells
+分子 #11: DNA (Cy5)
+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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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 FIELDBright-field microscopy / 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 |
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: 6243 / 平均露光時間: 2.5 sec. / 平均電子線量: 54.1 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
-原子モデル構築 1
初期モデル | Chain - Source name: PDB / Chain - Initial model type: experimental model |
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精密化 | 空間: REAL / プロトコル: AB INITIO MODEL / 当てはまり具合の基準: correlation coefficient |
得られたモデル | PDB-8ebt: |