SASDCA3: Zinc finger and BTB domain-containing protein 38 (ZBTB38) complex...

Basic information

• Entry: Database: SASBDB / ID: SASDCA3

Sample

Zinc finger and BTB domain-containing protein 38 (ZBTB38) complexed with methylated C-terminal ZBTB38 binding sequence

• Zinc finger and BTB domain-containing protein 38 (protein), ZBTB38, Homo sapiens
• methylated C-terminal ZBTB38 binding sequence (DNA), mZBTB38BS

Function / homology

Function:

methyl-CpG binding / regulation of DNA replication / chromosome / blood microparticle / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus

Domain/homology:

BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type

Component:

Zinc finger and BTB domain-containing protein 38

• Biological species: Homo sapiens (human)
• 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 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

• Jill Trewhella (School of Molecular Bioscience, University of Sydney., Sydney, New South Wales 2006, Australia)

Models

• Model #1238: ; Type: dummy / Software: (1.45) / Radius of dummy atoms: 2.75 A / Comment: ZBTB38(1006-1153)-mCZ38BS complex / Chi-square value: 1.268 / P-value: 0.123700; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1237: ; Type: atomic / Software: (2.2) / Symmetry: P1 / Comment: ZBTB38(1006-1153)-mCZ38BS complex / Chi-square value: 1.739 / P-value: 0.027726; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Zinc finger and BTB domain-containing protein 38 (ZBTB38) complexed with methylated C-terminal ZBTB38 binding sequence; Specimen concentration: 3.4 mg/ml / Entity id: 663 / 667
• 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 concentration step flow through

Entity #663

Name: ZBTB38 / Type: protein
Description: Zinc finger and BTB domain-containing protein 38
Formula weight: 17.337 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q8NAP3
Sequence:

TSRPYACELC AKQFQSPSTL KMHMRCHTGE KPYQCKTCGR CFSVQGNLQK HERIHLGLKE FVCQYCNKAF TLNETLKIHE RIHTGEKRYH CQFCFQRFLY LSTKRNHEQR HIREHNGKGY ACFQCPKICK TAAALGMHQK KHLFKSP

Entity #667

Name: mZBTB38BS / 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: Zinc finger and BTB domain-containing protein 38 (ZBTB38) complexed with methylated C-terminal ZBTB38 binding sequence
Measurement date: Nov 11, 2016 / Cell temperature: 22 °C / Exposure time: 30 sec. / Number of frames: 120 / Unit: 1/nm /

	Min	Max
Q	0.0813	3.3624

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 248 /

	Min	Max
Q	0.0812838	3.36238
P(R) point	1	248
R	0	8.18

Result

Type of curve: single_conc

	Experimental	Standard	Standard error	Porod
MW	34.389 kDa	46 kDa	12	33.3 kDa
Volume	-	-	-	49.87 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.1822	0.0016	0.18	0.0009
Radius of gyration, Rg	2.61 nm	0.03	2.5 nm	0.04

	Min	Max	Error
D	-	8.18	5
Guinier point	1	33	-