+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1kx5 | ||||||
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タイトル | X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution | ||||||
要素 |
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キーワード | STRUCTURAL PROTEIN/DNA (構造) / NUCLEOSOME (ヌクレオソーム) / CHROMATIN (クロマチン) / HISTONE (ヒストン) / PROTEIN-DNA INTERACTION (DNA結合タンパク質) / NUCLEOPROTEIN (核タンパク質) / SUPERCOILED DNA (DNA超らせん) / NUCLEOSOME CORE / PROTEIN-DNA COMPLEX (デオキシリボ核酸) / DNA BENDING / DNA CURVATURE / DNA-CATION BINDING / DNA-METAL BINDING / DNA SOLVATION / STRUCTURAL PROTEIN-DNA COMPLEX (構造) | ||||||
機能・相同性 | 機能・相同性情報 : / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Transcriptional regulation by small RNAs / chromatin organization => GO:0006325 / B-WICH complex positively regulates rRNA expression / HDACs deacetylate histones / chromatin organization => GO:0006325 ...: / : / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / Assembly of the ORC complex at the origin of replication / Transcriptional regulation by small RNAs / chromatin organization => GO:0006325 / B-WICH complex positively regulates rRNA expression / HDACs deacetylate histones / chromatin organization => GO:0006325 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / Senescence-Associated Secretory Phenotype (SASP) / PRC2 methylates histones and DNA / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / Oxidative Stress Induced Senescence / DNA replication-dependent chromatin assembly / nuclear chromosome / stem cell population maintenance / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / epigenetic regulation of gene expression / 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 / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNAメチル化 / Condensation of Prophase Chromosomes / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / DNA-templated transcription initiation / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / 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 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / 遺伝的組換え / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / ヌクレオソーム / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 遺伝子発現 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / protein domain specific binding / chromatin binding / クロマチン / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / 核質 / 生体膜 / 細胞核 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Xenopus laevis (アフリカツメガエル) | ||||||
手法 | X線回折 / シンクロトロン / フーリエ合成 / 解像度: 1.94 Å | ||||||
データ登録者 | Davey, C.A. / Sargent, D.F. / Luger, K. / Maeder, A.W. / Richmond, T.J. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2002 タイトル: Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution 著者: Davey, C.A. / Sargent, D.F. / Luger, K. / Maeder, A.W. / Richmond, T.J. #1: ジャーナル: Nature / 年: 1997 タイトル: Crystal structure of the nucleosome core particle at 2.8 A resolution 著者: Luger, K. / Maeder, A.W. / Richmond, R.K. / Sargent, D.F. / Richmond, T.J. #2: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2002 タイトル: DNA-dependent divalent cation binding in the nucleosome core particle. 著者: Davey, C.A. / Richmond, T.J. #3: ジャーナル: To be Published タイトル: DNA structure in the nucleosome core 著者: Richmond, T.J. / Davey, C.A. | ||||||
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 | 1kx5.cif.gz | 448 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1kx5.ent.gz | 340.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1kx5.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/kx/1kx5 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kx5 | 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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1 |
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単位格子 |
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-要素
-DNA鎖 , 2種, 2分子 IJ
#1: DNA鎖 | 分子量: 45368.051 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: palindromic 147 base pair DNA duplex with exception of position 0 由来: (組換発現) Homo sapiens (ヒト) 解説: DNA SEQUENCE SYNTHESIZED, CLONED, MULTIMERIZED, AND EXCISED FROM PLASMID; 発現宿主: Escherichia coli (大腸菌) |
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#2: DNA鎖 | 分子量: 45359.035 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: palindromic 147 base pair DNA duplex with exception of position 0 由来: (組換発現) Homo sapiens (ヒト) 解説: DNA SEQUENCE SYNTHESIZED, CLONED, MULTIMERIZED, AND EXCISED FROM PLASMID 発現宿主: Escherichia coli (大腸菌) |
-タンパク質 , 4種, 8分子 AEBFCGDH
#3: タンパク質 | 分子量: 15303.930 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P16105, UniProt: P84233*PLUS #4: タンパク質 | 分子量: 11263.231 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02304, UniProt: P62799*PLUS #5: タンパク質 | 分子量: 13907.163 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P06897 #6: タンパク質 | 分子量: 13848.097 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) Xenopus laevis (アフリカツメガエル) 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02281 |
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-非ポリマー , 3種, 3148分子
#7: 化合物 | ChemComp-MN / #8: 化合物 | ChemComp-CL / #9: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 44 |
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-試料調製
結晶 | マシュー密度: 2.59 Å3/Da / 溶媒含有率: 52.54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 詳細: manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 |
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結晶化 | *PLUS 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 103 K |
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-4 / 波長: 0.93 Å |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1999年5月18日 |
放射 | モノクロメーター: Si 111 CHANNEL / 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: 0.93 Å / 相対比: 1 |
反射 | 解像度: 1.94→20 Å / Num. all: 158096 / Num. obs: 151140 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / 冗長度: 5.1 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.072 |
反射 シェル | 解像度: 1.94→2.01 Å / Rmerge(I) obs: 0.291 / % possible all: 88 |
反射 | *PLUS 最低解像度: 20 Å |
反射 シェル | *PLUS % possible obs: 88 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: PDB entry 1AOI 解像度: 1.94→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2948930.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: 792 OF THE PROTEIN ATOMS HAVE ZERO OCCUPANCY. THESE INCLUDE DISORDERED PORTIONS OF THE N-TERMINAL TAIL REGIONS OF CHAINS A-H AND THE C-TERMINUS OF CHAINS C & G. THE AMINO ACIDS WITH ZERO ...詳細: 792 OF THE PROTEIN ATOMS HAVE ZERO OCCUPANCY. THESE INCLUDE DISORDERED PORTIONS OF THE N-TERMINAL TAIL REGIONS OF CHAINS A-H AND THE C-TERMINUS OF CHAINS C & G. THE AMINO ACIDS WITH ZERO OCCUPANCY ARE WITHIN RESIDUES 1-32 OF CHAIN A, 1-30 OF CHAIN E, 1-23 OF CHAIN B, 1-15 OF CHAIN F, 1-14 & 121-128 OF CHAIN C, 1-12 & 122-128 OF CHAIN G, 1-21 OF CHAIN D, AND 1-23 OF CHAIN H. THEY WERE INCLUDED IN THE REFINEMENT FOR STEREOCHEMICAL PURPOSES, BUT DID NOT CONTRIBUTE TO THE X-RAY TERM.
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原子変位パラメータ | Biso mean: 51.5 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.94→6 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.94→2.06 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最低解像度: 6 Å | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS 最低解像度: 2.01 Å / Rfactor Rfree: 0.374 / Rfactor Rwork: 0.341 |