+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4e5z | ||||||
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タイトル | Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair | ||||||
要素 |
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キーワード | DNA BINDING PROTEIN/DNA / BETA BARREL (Βバレル) / PROTEIN-DNA COMPLEX (デオキシリボ核酸) / DOUBLE HELIX / damage (損傷) / DNA repair (DNA修復) / Host-virus interactions / Protein ubiquitination / Proteosomal degradation / DNA BINDING PROTEIN-DNA complex | ||||||
機能・相同性 | 機能・相同性情報 positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / cullin family protein binding / viral release from host cell / pyrimidine dimer repair / ectopic germ cell programmed cell death / protein autoubiquitination / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / proteasomal protein catabolic process / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / TP53 Regulates Transcription of DNA Repair Genes / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wntシグナル経路 / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / 細胞結合 / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / Ub-specific processing proteases / DNA修復 / apoptotic process / DNA damage response / クロマチン / protein-containing complex binding / 核小体 / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / 核質 / 細胞核 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.22 Å | ||||||
データ登録者 | Yeh, J.I. / Du, S. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2012 タイトル: Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. 著者: Yeh, J.I. / Levine, A.S. / Du, S. / Chinte, U. / Ghodke, H. / Wang, H. / Shi, H. / Hsieh, C.L. / Conway, J.F. / Van Houten, B. / Rapic-Otrin, V. | ||||||
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 | 4e5z.cif.gz | 665.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4e5z.ent.gz | 539 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4e5z.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/e5/4e5z ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e5z | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 128478.914 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: DDB1, DDB1_HUMAN, Q16531, XAP1 プラスミド: pBlueBac4.5/V5-His NT-His10-DDB1pBlueBac4.5/V5-His NT-His10-DDB1 細胞株 (発現宿主): Sf9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q16531 |
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#2: タンパク質 | 分子量: 49059.004 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: DDB2 / プラスミド: pBlueBac4.5/V5-HisNT-FLAG-DDB2 / 細胞株 (発現宿主): Sf9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q92466 |
#3: DNA鎖 | 分子量: 7424.801 Da / 分子数: 1 / 由来タイプ: 合成 詳細: Synthetic single stranded 24-oligodeoxynucleotides with complementary strand sequence: 5-TGACTGTATGATGACGATGCTGAC-3 |
#4: DNA鎖 | 分子量: 7189.646 Da / 分子数: 1 / 由来タイプ: 合成 詳細: Synthetic single stranded oligodeoxynucleotides with a central tetrahydrofuran abasic site mimic (3DR) on coding strand with sequence: 5-GTCAGCATCG(3DR)CATCATACAGTCA-3 |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 3 |
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-試料調製
結晶 | マシュー密度: 2.81 Å3/Da / 溶媒含有率: 56.19 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法 / pH: 7.5 詳細: 20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr ...詳細: 20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 23-ID-D |
検出器 | タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2009年7月8日 / 詳細: monochromators |
放射 | モノクロメーター: SAGITALLY FOCUSED Si(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
反射 | 解像度: 3.2→41.093 Å / Num. all: 36260 / Num. obs: 33928 / % possible obs: 77.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 5.6 % / Biso Wilson estimate: 38.09 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.105 / Net I/σ(I): 10.9 |
反射 シェル | 解像度: 3.2→3.31 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.358 / % possible all: 77.8 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 3EI2 解像度: 3.22→41.093 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU ML: 0.44 / σ(F): 0 / 位相誤差: 30.96 / 立体化学のターゲット値: MLHL 詳細: THE MODEL WAS REFINED USING ITERATIVE CYCLES OF TLS AND RESTRAINED REFINEMENT (INCLUDING SECONDARY STRUCTURE, GEOMETRY, AND TORSION ANGLE RESTRAINTS) THROUGH PHENIX. CAREFUL INSPECTION OF ...詳細: THE MODEL WAS REFINED USING ITERATIVE CYCLES OF TLS AND RESTRAINED REFINEMENT (INCLUDING SECONDARY STRUCTURE, GEOMETRY, AND TORSION ANGLE RESTRAINTS) THROUGH PHENIX. CAREFUL INSPECTION OF WEIGHTED AND UNWEIGHTED MAPS, IN PARTICULAR, THE DIFFERENCE FOURIER MAPS, AFTER EACH REFINEMENT ROUND VERIFIED CORRECTNESS OF REGIONS MODIFIED OR EXTENDED IN THE PREVIOUS CYCLE. PROGRAMMATIC DIFFERENCES IN THE APPLICATION AND SCALING OF TLS PARAMETERS MAY RESULT IN VARIATIONS IN THE MAPS CALCULATED USING THE SF DIRECTLY DOWNLOADED FROM THE DATABASE. CALCULATING STRUCTURE FACTORS (SF) USING MODEL COORDINATES AND THERMAL PARAMETERS FROM THE DEPOSITED PDB FILES IN PHENIX WILL REPRODUCE THE MAPS AND CONFORMATIONAL FEATURES DESCRIBED BY THE AUTHORS IN THE CITATION.
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 185.363 Å2
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精密化ステップ | サイクル: LAST / 解像度: 3.22→41.093 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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