- PDB-2ig0: Structure of 53BP1/methylated histone peptide complex -
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基本情報
登録情報
データベース: PDB / ID: 2ig0
タイトル
Structure of 53BP1/methylated histone peptide complex
要素
Dimethylated Histone H4-K20 peptide
Tumor suppressor p53-binding protein 1
キーワード
CELL CYCLE / TANDEM TUDOR DOMAINS / DIMETHYLATED HISTONE H4 / DNA REPAIR / CELL CYCLE REGULATION
機能・相同性
機能・相同性情報
ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of megakaryocyte differentiation / negative regulation of double-strand break repair via homologous recombination ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of megakaryocyte differentiation / negative regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / histone reader activity / Meiotic synapsis / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / DNA damage checkpoint signaling / PRC2 methylates histones and DNA / replication fork / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / protein homooligomerization / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / kinetochore / PKMTs methylate histone lysines / Meiotic recombination / positive regulation of DNA-binding transcription factor activity / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / site of double-strand break / HATs acetylate histones / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / protein heterodimerization activity / Amyloid fiber formation / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm 類似検索 - 分子機能
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
波長: 0.9795 Å / 相対比: 1
反射
解像度: 1.7→24.11 Å / Num. all: 11776 / Num. obs: 11776 / % possible obs: 82.96 %
反射 シェル
解像度: 1.7→1.744 Å / % possible all: 30.34
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.2.0019
精密化
HKL-2000
データ収集
HKL-2000
データ削減
HKL-2000
データスケーリング
MOLREP
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 1.7→24.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.55 / SU ML: 0.096 / 交差検証法: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.155 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.25138
629
5.1 %
RANDOM
Rwork
0.1759
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obs
0.1798
11775
82.96 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK