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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 | ||||||
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![]() | TRANSFERASE / Ternary structure of DIM-5 / a SUV39-type histone-H3 Lys-9 methyltransferase / SET domain protein forms a knot-like substructure / 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 | ![]() chromatin organization => GO:0006325 / [histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication ...chromatin organization => GO:0006325 / [histone H3]-lysine9 N-trimethyltransferase / histone H3K9 trimethyltransferase activity / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / replication fork protection complex / Oxidative Stress Induced Senescence / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / 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 methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / methylation / double-stranded DNA binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / protein-containing complex / DNA binding / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Zhang, X. / Yang, Z. / Khan, S.I. / Horton, J.R. / Tamaru, H. / Selker, E.U. / Cheng, X. | ||||||
![]() | ![]() 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: ![]() ![]() |
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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 | ![]() | 113.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 81.4 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 | ![]() | 517.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 549.9 KB | 表示 | |
XML形式データ | ![]() | 15.2 KB | 表示 | |
CIF形式データ | ![]() | 22.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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 |
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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: 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) ![]() ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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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: ![]() 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 |