+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4h9n | ||||||
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タイトル | Complex structure 1 of DAXX/H3.3(sub5)/H4 | ||||||
要素 |
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キーワード | DNA BINDING PROTEIN/APOPTOSIS / histone chaperone / DNA BINDING PROTEIN-APOPTOSIS complex | ||||||
機能・相同性 | 機能・相同性情報 cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / transcription regulator inhibitor activity / oocyte maturation / nuclear androgen receptor binding / nucleus organization / protein kinase activator activity / androgen receptor signaling pathway / spermatid development / regulation of protein ubiquitination / chromosome, centromeric region / extrinsic apoptotic signaling pathway via death domain receptors / cellular response to unfolded protein / single fertilization / subtelomeric heterochromatin formation / positive regulation of protein kinase activity / negative regulation of megakaryocyte differentiation / RNA polymerase II core promoter sequence-specific DNA binding / 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 / JNK cascade / heat shock protein binding / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / cellular response to copper ion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / cellular response to cadmium ion / telomere organization / embryo implantation / Meiotic synapsis / RNA Polymerase I Promoter Opening / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / SUMOylation of transcription cofactors / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / 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 / G2/M DNA damage checkpoint / HDMs demethylate histones / multicellular organism growth / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / PML body / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / osteoblast differentiation / Transcriptional regulation of granulopoiesis / male gonad development / structural constituent of chromatin / transcription corepressor activity / nucleosome / p53 binding / Regulation of TP53 Degradation / 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 / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / cellular response to heat / Processing of DNA double-strand break ends / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth 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: 1.95 Å | ||||||
データ登録者 | Elsasser, S.J. / Huang, H. / Lewis, P.W. / Chin, J.W. / Allis, D.C. / Patel, D.J. | ||||||
引用 | ジャーナル: To be Published タイトル: DAXX chaperone envelops an H3.3/H4 dimer dictating H3.3-specific read out 著者: Elsasser, S.J. / Huang, H. / Lewis, P.W. / Chin, J.W. / Allis, D.C. / Patel, D.J. | ||||||
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 | 4h9n.cif.gz | 178.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4h9n.ent.gz | 141.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4h9n.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
文書・要旨 | 4h9n_validation.pdf.gz | 450.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4h9n_full_validation.pdf.gz | 452.4 KB | 表示 | |
XML形式データ | 4h9n_validation.xml.gz | 19.4 KB | 表示 | |
CIF形式データ | 4h9n_validation.cif.gz | 28.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/h9/4h9n ftp://data.pdbj.org/pub/pdb/validation_reports/h9/4h9n | HTTPS FTP |
-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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 15257.816 Da / 分子数: 1 / 変異: S96A, Y99F, G102A, A111T, M120F / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P84243 | ||
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#2: タンパク質 | 分子量: 11263.231 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: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, ...遺伝子: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62805 | ||
#3: タンパク質 | 分子量: 24725.328 Da / 分子数: 1 / Fragment: UNP residues 178-389 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DAXX, BING2, DAP6 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UER7 | ||
#4: 化合物 | ChemComp-PO4 / #5: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.55 Å3/Da / 溶媒含有率: 51.74 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: 1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-データ収集
放射光源 | 由来: シンクロトロン / サイト: NSLS / ビームライン: X29A / 波長: 0.979 Å |
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放射 | 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: 0.979 Å / 相対比: 1 |
反射 | 解像度: 1.95→50 Å / Num. all: 39270 / Num. obs: 39270 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-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 / 解像度: 1.95→48.058 Å / SU ML: 0.42 / σ(F): 1.36 / σ(I): 5.1 / 位相誤差: 20.42 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 44.673 Å2 / ksol: 0.364 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 1.95→48.058 Å
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拘束条件 |
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LS精密化 シェル |
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