6ML6

ZBTB24 Zinc Fingers 4-8 with 19+1mer DNA Oligonucleotide (Sequence 4 with a CpA 5mC Modification)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of specific DNA binding by the transcription factor ZBTB24.

Ren, R.Hardikar, S.Horton, J.R.Lu, Y.Zeng, Y.Singh, A.K.Lin, K.Coletta, L.D.Shen, J.Lin Kong, C.S.Hashimoto, H.Zhang, X.Chen, T.Cheng, X.

(2019) Nucleic Acids Res 47: 8388-8398

  • DOI: 10.1093/nar/gkz557
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • ZBTB24, encoding a protein of the ZBTB family of transcriptional regulators, is one of four known genes-the other three being DNMT3B, CDCA7 and HELLS-that are mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a ...

    ZBTB24, encoding a protein of the ZBTB family of transcriptional regulators, is one of four known genes-the other three being DNMT3B, CDCA7 and HELLS-that are mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a genetic disorder characterized by DNA hypomethylation and antibody deficiency. The molecular mechanisms by which ZBTB24 regulates gene expression and the biological functions of ZBTB24 are poorly understood. Here, we identified a 12-bp consensus sequence [CT(G/T)CCAGGACCT] occupied by ZBTB24 in the mouse genome. The sequence is present at multiple loci, including the Cdca7 promoter region, and ZBTB24 binding is mostly associated with gene activation. Crystallography and DNA-binding data revealed that the last four of the eight zinc fingers (ZFs) (i.e. ZF5-8) in ZBTB24 confer specificity of DNA binding. Two ICF missense mutations have been identified in the ZBTB24 ZF domain, which alter zinc-binding cysteine residues. We demonstrated that the corresponding C382Y and C407G mutations in mouse ZBTB24 abolish specific DNA binding and fail to induce Cdca7 expression. Our analyses indicate and suggest a structural basis for the sequence specific recognition by a transcription factor centrally important for the pathogenesis of ICF syndrome.


    Organizational Affiliation

    Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger and BTB domain-containing protein 24A151Mus musculusMutation(s): 0 
Gene Names: Zbtb24Bif1Bsg1Znf450
Find proteins for Q80X44 (Mus musculus)
Explore Q80X44 
Go to UniProtKB:  Q80X44
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*GP*(5CM)P*AP*GP*GP*TP*CP*CP*TP*GP*GP*AP*CP*GP*AP*AP*TP*T)-3')E20Mus musculus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*AP*TP*TP*CP*GP*TP*CP*CP*AP*GP*GP*AP*CP*CP*TP*GP*CP*G)-3')F20Mus musculus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, E, F
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.163α = 90
b = 68.244β = 92.9
c = 49.259γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence