4M9E | pdb_00004m9e

Structure of Klf4 zinc finger DNA binding domain in complex with methylated DNA

• PDB DOI: https://doi.org/10.2210/pdb4M9E/pdb
• NAKB: 4M9E

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-14 Released: 2014-02-12 
• Deposition Author(s): Liu, Y., Olanrewaju, Y.O., Blumenthal, R.M., Zhang, X., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.234 (Depositor) 
• R-Value Work: 
  0.187 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structural basis for Klf4 recognition of methylated DNA.

Liu, Y., Olanrewaju, Y.O., Zheng, Y., Hashimoto, H., Blumenthal, R.M., Zhang, X., Cheng, X.

(2014) Nucleic Acids Res 42: 4859-4867

• PubMed: 24520114 
• DOI: https://doi.org/10.1093/nar/gku134
• Primary Citation Related Structures: 
  4M9E


• PubMed Abstract: 
  

  Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg-Glu pair.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA and Department of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.9 kDa 
• Atom Count: 1,279 
• Modeled Residue Count: 105 
• Deposited Residue Count: 108 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Krueppel-like factor 4	A	88	Mus musculus	Mutation(s): 0  Gene Names: Klf4, Ezf, Gklf, Zie
UniProt
Find proteins for Q60793 (Mus musculus) Explore Q60793  Go to UniProtKB:  Q60793

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*GP*GP*(5CM)P*GP*TP*GP*GP*C)-3')	B	10	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*AP*(5CM)P*GP*CP*CP*TP*C)-3')	C	10	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.234 (Depositor) 
• R-Value Work:  0.187 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.705	α = 90
b = 48.705	β = 90
c = 131.015	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Liu, Y., Olanrewaju, Y.O., Blumenthal, R.M., Zhang, X., Cheng, X.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references
• Version 1.2: 2014-05-21
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description