+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDCB3 |
---|---|
Sample | Methylated C-terminal ZBTB38 binding sequence (mCZ38BS)
|
Citation | Journal: J Mol Biol / Year: 2018 Title: The C-Terminal Zinc Fingers of ZBTB38 are Novel Selective Readers of DNA Methylation. Authors: Amir Pozner / Nicholas O Hudson / Jill Trewhella / Tommy W Terooatea / Sven A Miller / Bethany A Buck-Koehntop / Abstract: Methyl-CpG binding proteins play an essential role in translating DNA methylation marks into a downstream transcriptional response, which has implications for both normal cell function as well as ...Methyl-CpG binding proteins play an essential role in translating DNA methylation marks into a downstream transcriptional response, which has implications for both normal cell function as well as disease. Although for many of these proteins, a detailed mechanistic understanding for how this cellular process is mediated remains to be determined. ZBTB38 is an under-characterized member of the zinc finger (ZF) family of methyl-CpG binding proteins. Functional knowledge has been gained for its conserved methylated DNA binding N-terminal ZF region; however, a specific role for the C-terminal set of five ZFs remains to be elucidated. Here we demonstrate for the first time that a subset of the C-terminal ZBTB38 ZFs exhibit high-affinity DNA interactions and that preferential targeting of the consensus DNA site is methyl specific. Utilizing a hybrid approach, a model for the C-terminal ZBTB38 ZFs in complex with its cognate DNA target is proposed, providing insight into a possible novel mode of methylated DNA recognition. Furthermore, it is shown that the C-terminal ZFs of ZBTB38 can directly occupy promoters harboring the newly identified sequence motif in cell in a methyl-dependent manner and, depending on the gene context, contribute to modulating transcriptional response. Combined, these findings provide evidence for a key and novel physiological function for the C-terminal ZF domain of ZBTB38. |
Contact author |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Models
Model #1236 | Type: dummy / Radius of dummy atoms: 2.40 A / Comment: methylated C-terminal ZBTB38 binding sequence / Chi-square value: 1.121 / P-value: 0.848600 Search similar-shape structures of this assembly by Omokage search (details) |
---|
-Sample
Sample | Name: Methylated C-terminal ZBTB38 binding sequence (mCZ38BS) Specimen concentration: 4.2 mg/ml |
---|---|
Buffer | Name: 10 mM Tris, 1 mM tris(2-carboxy-ethyl)phosphine (TCEP), 0.05% NaN3, 10% D2O pH: 6.8 Comment: Solvent blank taken from flow through in concentration step |
Entity #666 | Name: mCZ38BS / Type: DNA / Description: methylated C-terminal ZBTB38 binding sequence / Formula weight: 16.705 / Num. of mol.: 1 Sequence: GCACTCATCG GCGCAGATCA GCTAGCCGGC TAGCTGATCT GCGCCGATGA GTGC |
-Experimental information
Beam | Instrument name: Department of Chemistry, University of Utah Anton Paar SAXSess City: Salt Lake City, UT / 国: USA / Type of source: X-ray in house / Wavelength: 0.154 Å / Dist. spec. to detc.: 0.2612 mm | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Name: Dectris Mythen 1K / Type: 1D diode array detector / Pixsize x: 50 mm | ||||||||||||||||||||||||||||||||||||
Scan | Title: methylated C-terminal ZBTB38 binding sequence (mCZ38BS) Measurement date: Oct 27, 2016 / Cell temperature: 22 °C / Exposure time: 30 sec. / Number of frames: 120 / Unit: 1/nm /
| ||||||||||||||||||||||||||||||||||||
Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 475 /
| ||||||||||||||||||||||||||||||||||||
Result | Type of curve: single_conc
|