+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1h89 | ||||||
---|---|---|---|---|---|---|---|
タイトル | CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION REGULATION / BZIP / PROTO-ONCOGENE / MYB / C-MYB / C/EBP / TRANSCRIPTION-DNA complex | ||||||
機能・相同性 | ![]() C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of testosterone secretion / positive regulation of biomineral tissue development / myeloid cell development / positive regulation of hepatic stellate cell proliferation / integrated stress response signaling ...C/EBP complex / granuloma formation / regulation of odontoblast differentiation / CHOP-C/EBP complex / positive regulation of sodium-dependent phosphate transport / positive regulation of testosterone secretion / positive regulation of biomineral tissue development / myeloid cell development / positive regulation of hepatic stellate cell proliferation / integrated stress response signaling / T-helper 1 cell activation / Response of EIF2AK1 (HRI) to heme deficiency / hepatocyte proliferation / positive regulation of hepatic stellate cell activation / positive regulation of transforming growth factor beta production / ATF4 activates genes in response to endoplasmic reticulum stress / regulation of osteoclast differentiation / embryonic digestive tract development / stem cell division / mammary gland epithelial cell differentiation / myeloid cell differentiation / condensed chromosome, centromeric region / regulation of dendritic cell differentiation / cellular response to interleukin-6 / regulation of interleukin-6 production / WD40-repeat domain binding / mammary gland epithelial cell proliferation / histone acetyltransferase binding / positive regulation of interleukin-4 production / regulation of cell differentiation / ubiquitin-like protein ligase binding / Response of EIF2AK4 (GCN2) to amino acid deficiency / Transcriptional Regulation by VENTX / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of collagen biosynthetic process / embryonic placenta development / positive regulation of fat cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of osteoblast differentiation / Nuclear events stimulated by ALK signaling in cancer / brown fat cell differentiation / negative regulation of T cell proliferation / ovarian follicle development / positive regulation of glial cell proliferation / spleen development / response to endoplasmic reticulum stress / B cell differentiation / thymus development / cellular response to leukemia inhibitory factor / acute-phase response / liver regeneration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / neuron differentiation / chromatin DNA binding / kinase binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / calcium ion transport / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / positive regulation of cold-induced thermogenesis / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / response to lipopolysaccharide / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / inflammatory response / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Tahirov, T.H. / Ogata, K. | ||||||
![]() | ![]() タイトル: Mechanism of C-Myb-C/Ebpbeta Cooperation from Separated Sites on a Promoter 著者: Tahirov, T.H. / Sato, K. / Ichikawa-Iwata, E. / Sasaki, M. / Inoue-Bungo, T. / Shiina, M. / Kimura, K. / Takata, S. / Fujikawa, A. / Morii, H. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K. #1: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2001 タイトル: Crystals of Ternary Protein-DNA Complexes Composed of DNA-Binding Domains C-Myb or V-Myb, C/Ebpalpha or C/Ebpbeta and Tom-1A Promoter Fragment 著者: Tahirov, T.H. / Inoue, T. / Sasaki, M. / Shiina, M. / Kimura, K. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Kamiya, N. / Ogata, K. #2: ![]() タイトル: Crystal Structures of C-Myb DNA-Binding Domain in Free State: An Evidence for Binding of Na+ and Comparison with Solution Structure Runt Domain, Cbfbeta and the C/Ebpbeta bZIP Region 著者: Tahirov, T.H. / Morii, H. / Uedaira, H. / Sasaki, M. / Sarai, A. / Adachi, S. / Park, S.Y. / Kamiya, N. / Ogata, K. #3: ![]() タイトル: Structural Analyses of DNA Recognition by the Aml1/ Runx-1 Runt Domain and its Allosteric Control by Cbfbeta 著者: Tahirov, T.H. / Inoue-Bungo, T. / Morii, H. / Fujikawa, A. / Sasaki, M. / Kimura, K. / Shiina, M. / Sato, K. / Kumasaka, T. / Yamamoto, M. / Ishii, S. / Ogata, K. | ||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 101.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 72.8 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 | ![]() | 446.6 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 457.7 KB | 表示 | |
XML形式データ | ![]() | 14.9 KB | 表示 | |
CIF形式データ | ![]() | 20.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
| ||||||||
詳細 | OF C/EBP BETA AND MONOMER OF MYB PROTO- ONCOGENE PROTEINBOUND TO A DUPLEX DNA FRAGMENTFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 THE |
-
要素
-タンパク質 , 2種, 3分子 ABC
#1: タンパク質 | 分子量: 7823.048 Da / 分子数: 2 / 断片: RESIDUES 273-336 / 由来タイプ: 組換発現 / 詳細: BZIP DOMAIN / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | | 分子量: 19173.074 Da / 分子数: 1 / 断片: RESIDUES 35-193 / Mutation: YES / 由来タイプ: 組換発現 / 詳細: DNA BINDING DOMAIN / 由来: (組換発現) ![]() ![]() ![]() ![]() |
---|
-DNA鎖 , 2種, 2分子 DE
#3: DNA鎖 | 分子量: 8028.177 Da / 分子数: 1 / 断片: FRAGMENT FROM TOM-1A PROMOTER / 由来タイプ: 合成 / 由来: (合成) ![]() |
---|---|
#4: DNA鎖 | 分子量: 7948.129 Da / 分子数: 1 / 断片: FRAGMENT FROM TOM-1A PROMOTER / 由来タイプ: 合成 / 由来: (合成) ![]() |
-非ポリマー , 2種, 125分子 ![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: 化合物 | #6: 水 | ChemComp-HOH / | |
---|
-詳細
構成要素の詳細 | CHAIN C ENGINEERED MUTATION LYS35MET, ARG36GLY C/EBP BETA IS IMPORTANT TRANSCRIPTIONAL ACTIVATOR IN ...CHAIN C ENGINEERED |
---|---|
配列の詳細 | LYS 35 WAS REPLACED BY MET AND ARG 36 WAS REPLACED BY GLY BECAUSE OF EXPRESSION |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 3.66 Å3/Da / 溶媒含有率: 65.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | 温度: 297 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 詳細: 0.1 M KCL, 0.05 MGSO4, 4% V/V MPD, 6% V/V GLYCEROL, 0.05 M NA HEPES PH 7.0 AT 24 DEGREES C | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 297 K / pH: 6.8 / 手法: 蒸気拡散法, シッティングドロップ法詳細: Tahirov, T.H., (2001) Acta Crystallogr.,Sect.D, 57, 1655. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
|
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 1998年11月17日 / 詳細: MIRRORS |
放射 | モノクロメーター: DIAMOND / 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: 1.04 Å / 相対比: 1 |
反射 | 解像度: 2.45→20 Å / Num. obs: 27451 / % possible obs: 99 % / Observed criterion σ(I): 0 / 冗長度: 7.496 % / Biso Wilson estimate: 67 Å2 / Rsym value: 0.072 / Net I/σ(I): 27.5043 |
反射 シェル | 解像度: 2.45→2.54 Å / 冗長度: 4 % / Mean I/σ(I) obs: 2.162 / Rsym value: 0.397 / % possible all: 95.5 |
反射 | *PLUS 最高解像度: 2.45 Å / 最低解像度: 20 Å / Observed criterion σ(I): 0 / Num. measured all: 205777 / Rmerge(I) obs: 0.072 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: 1H88 解像度: 2.45→19.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 979672.69 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: BULK SOLVENT MODEL USED. ATOMS C, O, N, CA AND CB ARE HARMONICALLY RESTRAINED DURING REFINEMENT WITH HARMONIC RESTRAINT CONSTANT OF 100
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 38.0889 Å2 / ksol: 0.292803 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 65.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.45→19.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.45→2.6 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: CNS / バージョン: 0.9 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最低解像度: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
|