+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1peg | ||||||
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タイトル | Structural basis for the product specificity of histone lysine methyltransferases | ||||||
要素 |
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キーワード | TRANSFERASE (転移酵素) / Ternary structure of DIM-5 / a SUV39-type histone-H3 Lys-9 methyltransferase / SET domain protein forms a knot-like substructure (定義域 (データベース)) / pre-SET triangular Zn3Cys9 zinc cluster / post-SET zinc-binding site / a hybrid beta sheet formed by DIM-5 and H3 tail | ||||||
機能・相同性 | 機能・相同性情報 SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxidative Stress Induced Senescence / chromatin organization => GO:0006325 / [histone H3]-lysine9 N-trimethyltransferase / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / histone H3K9 trimethyltransferase activity / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair ...SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Oxidative Stress Induced Senescence / chromatin organization => GO:0006325 / [histone H3]-lysine9 N-trimethyltransferase / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / histone H3K9 trimethyltransferase activity / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / replication fork protection complex / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Chromatin modifying enzymes / CENP-A containing nucleosome / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNAメチル化 / 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 / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / 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 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / 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 / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / ヌクレオソーム / 遺伝子発現 / メチル化 / 染色体 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / double-stranded DNA binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / 核質 / 生体膜 / 細胞核 類似検索 - 分子機能 | ||||||
生物種 | Neurospora crassa (アカパンカビ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.59 Å | ||||||
データ登録者 | Zhang, X. / Yang, Z. / Khan, S.I. / Horton, J.R. / Tamaru, H. / Selker, E.U. / Cheng, X. | ||||||
引用 | ジャーナル: Mol.Cell / 年: 2003 タイトル: Structural basis for the product specificity of histone lysine methyltransferases 著者: Zhang, X. / Yang, Z. / Khan, S.I. / Horton, J.R. / Tamaru, H. / Selker, E.U. / Cheng, X. | ||||||
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 | 1peg.cif.gz | 113.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1peg.ent.gz | 81.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1peg.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/pe/1peg ftp://data.pdbj.org/pub/pdb/validation_reports/pe/1peg | HTTPS FTP |
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-関連構造データ
関連構造データ | 1ml9S S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 34111.551 Da / 分子数: 2 / 断片: residues 17-318 / 由来タイプ: 組換発現 由来: (組換発現) Neurospora crassa (アカパンカビ) プラスミド: pXC379 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) Codon plus RIL (Stratagene) / キーワード: wild-type DIM-5 参照: UniProt: Q8X225, ヒストンメチルトランスフェラーゼ #2: タンパク質・ペプチド | 分子量: 1565.797 Da / 分子数: 2 / 断片: residues 1-15 / 由来タイプ: 合成 詳細: The histone H3 peptide (N-terminal residues 1-15) is synthesized. 参照: UniProt: P02303, UniProt: P68431*PLUS #3: 化合物 | ChemComp-ZN / #4: 化合物 | |
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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: 1 |
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-試料調製
結晶 | マシュー密度: 2.58 Å3/Da / 溶媒含有率: 52.36 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 289 K / pH: 8.4 詳細: PEG 2000 monomethyl ether, trimethylamine, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 8.40 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 16 ℃ / pH: 9.8 / 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: NSLS / ビームライン: X25 / 波長: 1 |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2002年11月22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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.59→35 Å / Num. obs: 21803 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / 冗長度: 4.5 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 23.3 |
反射 シェル | 解像度: 2.59→2.68 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.228 / % possible all: 67.6 |
反射 | *PLUS 最高解像度: 2.59 Å / 最低解像度: 35 Å |
反射 シェル | *PLUS % possible obs: 67.6 % / Num. unique obs: 1578 / Mean I/σ(I) obs: 4.5 |
-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: PDB ENTRY 1ML9 解像度: 2.59→30.9 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 詳細: THE NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINS WERE IMPOSED ON THE TWO COMPLEXES DURING THE REFINEMENT, EXCEPT THE POST-SET REGION RESIDUES 53 TO 100. MOLECULE B IS VERY FLEXIBLE IN THIS REGION ...詳細: THE NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINS WERE IMPOSED ON THE TWO COMPLEXES DURING THE REFINEMENT, EXCEPT THE POST-SET REGION RESIDUES 53 TO 100. MOLECULE B IS VERY FLEXIBLE IN THIS REGION (ONLY THE CA ATOMS ARE GIVEN FOR THE RESIDUES 53 TO 87), WHILE THE CORRESPONDING REGION IN MOLECULE A IS ORDERED.
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原子変位パラメータ | Biso mean: 58.9 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: 2.59→30.9 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.59→2.74 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最低解像度: 35 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.68 Å / Rfactor Rwork: 0.3 |