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基本情報
登録情報 | データベース: PDB / ID: 9inc | ||||||
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タイトル | High resolutional Crystal Structure of human H2A.Z-H2B dimer in complex with human YL1-Z domain | ||||||
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![]() | NUCLEAR PROTEIN / Histones and its chaperone | ||||||
機能・相同性 | ![]() histone chaperone activity / regulation of double-strand break repair / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / somatic stem cell population maintenance / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding ...histone chaperone activity / regulation of double-strand break repair / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / somatic stem cell population maintenance / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of double-strand break repair via homologous recombination / protein localization to CENP-A containing chromatin / heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / transcription initiation-coupled chromatin remodeling / innate immune response in mucosa / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / cellular response to estradiol stimulus / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / euchromatin / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / antimicrobial humoral immune response mediated by antimicrobial peptide / HCMV Early Events / structural constituent of chromatin / antibacterial humoral response / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / defense response to Gram-negative bacterium / Oxidative Stress Induced Senescence / regulation of apoptotic process / killing of cells of another organism / Estrogen-dependent gene expression / histone binding / defense response to Gram-positive bacterium / regulation of cell cycle / Ub-specific processing proteases / nuclear speck / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Tan, W.S. / Liu, Y. / Hong, J.J. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis of human histone variant H2AZ recognized by human YL1 providing a conserved structural mechanism 著者: Tan, W.S. / Liu, Y. / Hong, J.J. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 195.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 156.1 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 466.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 470.1 KB | 表示 | |
XML形式データ | ![]() | 21.8 KB | 表示 | |
CIF形式データ | ![]() | 29.2 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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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: 10521.134 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 10421.904 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #3: タンパク質 | 分子量: 9567.714 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: 水 | ChemComp-HOH / | Has protein modification | N | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.15 Å3/Da / 溶媒含有率: 42.8 % |
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結晶化 | 温度: 289.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 45% PEG200 0.1 M HEPES pH 7.5 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年4月18日 |
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: 0.97918 Å / 相対比: 1 |
反射 | 解像度: 2.01→85.68 Å / Num. obs: 35203 / % possible obs: 100 % / 冗長度: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13.1 |
反射 シェル | 解像度: 2.01→2.06 Å / 冗長度: 9 % / Rmerge(I) obs: 1.574 / Num. unique obs: 2574 / CC1/2: 0.593 / % possible all: 100 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]()
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.01→39.77 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 / Origin x: -20.1703 Å / Origin y: -23.0867 Å / Origin z: -8.9141 Å
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精密化 TLSグループ | Selection details: all |