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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1jk2 | ||||||
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タイトル | Zif268 D20A mutant bound to the GCT DNA site | ||||||
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![]() | TRANSCRIPTION/DNA / zinc-finger / double stranded DNA / protein-DNA complex / TRANSCRIPTION-DNA COMPLEX | ||||||
機能・相同性 | ![]() glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process ...glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / regulation of progesterone biosynthetic process / regulation of protein sumoylation / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / positive regulation of post-translational protein modification / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / hemi-methylated DNA-binding / positive regulation of gene expression via chromosomal CpG island demethylation / interleukin-1-mediated signaling pathway / histone acetyltransferase binding / : / positive regulation of smooth muscle cell migration / skeletal muscle cell differentiation / locomotor rhythm / T cell differentiation / estrous cycle / RNA polymerase II core promoter sequence-specific DNA binding / BMP signaling pathway / long-term memory / response to glucose / regulation of neuron apoptotic process / positive regulation of chemokine production / positive regulation of interleukin-1 beta production / response to ischemia / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / regulation of long-term neuronal synaptic plasticity / circadian regulation of gene expression / response to insulin / negative regulation of canonical Wnt signaling pathway / cellular response to gamma radiation / positive regulation of miRNA transcription / positive regulation of neuron apoptotic process / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / sequence-specific DNA binding / learning or memory / response to hypoxia / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Miller, J.C. / Pabo, C.O. | ||||||
![]() | ![]() タイトル: Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. 著者: Miller, J.C. / Pabo, C.O. #1: ![]() タイトル: Zif268 Protein-DNA Complex Refined at 1.6 A: A Model System for Understanding Zinc Finger-DNA Interactions 著者: Elrod-Erickson, M. / Rould, M.A. / Nekludova, L. / Pabo, C.O. #2: ![]() タイトル: Binding Studies with Mutants of Zif268. Contribution of Individual Side Chains to Binding Affinity and Specificity in the Zif268 Zinc Finger-DNA Complex 著者: Elrod-Erickson, M. / Pabo, C.O. | ||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR |
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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 | ![]() | 50.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 33.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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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: DNA鎖 | 分子量: 3430.233 Da / 分子数: 1 / 由来タイプ: 合成 | ||
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#2: DNA鎖 | 分子量: 3279.151 Da / 分子数: 1 / 由来タイプ: 合成 | ||
#3: タンパク質 | 分子量: 10809.488 Da / 分子数: 1 / Fragment: ZINC FINGERS (Residues 333-421) / Mutation: D120A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() | ||
#4: 化合物 | #5: 水 | ChemComp-HOH / | |
-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: 2.25 Å3/Da / 溶媒含有率: 45.44 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: 300 mM NaCl, 10% PEG 1450, 25 mM Bis-Tris propane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 |
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結晶化 | *PLUS pH: 6.2 / 詳細: Elrod-Erickson, M., (1998) Structure, 6,451. | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 125 K |
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放射光源 | 由来: ![]() |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 1999年5月28日 / 詳細: Yale mirrors |
放射 | モノクロメーター: yale mirrors / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.65→20 Å / Num. all: 18149 / Num. obs: 18149 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.052 |
反射 シェル | 解像度: 1.65→1.71 Å / Num. unique all: 1460 / % possible all: 75.1 |
反射 | *PLUS Num. measured all: 138650 |
反射 シェル | *PLUS % possible obs: 75.1 % |
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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: D20A bound to the wt site with the appropriate change to the DNA and with waters and side chains of residues 18 and 21 removed 解像度: 1.65→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2 立体化学のターゲット値: X-PLOR parameters PARHCSDX.PRO and PARNDBX.DNA
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原子変位パラメータ | Biso mean: 30.1 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: 1.65→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.65→1.75 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 30.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.434 / % reflection Rfree: 10 % / Rfactor Rwork: 0.395 |