4GZN | pdb_00004gzn

Mouse ZFP57 zinc fingers in complex with methylated DNA

• PDB DOI: https://doi.org/10.2210/pdb4GZN/pdb
• NAKB: 4GZN

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


• Deposited: 2012-09-06 Released: 2012-10-17 
• Deposition Author(s): Liu, Y., Zhang, X., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free: 
  0.140 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.131 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.132 (Depositor) 

Literature

An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence.

Liu, Y., Toh, H., Sasaki, H., Zhang, X., Cheng, X.

(2012) Genes Dev 26: 2374-2379

• PubMed: 23059534 
• DOI: https://doi.org/10.1101/gad.202200.112
• Primary Citation Related Structures: 
  4GZN


• PubMed Abstract: 
  

  Zinc finger transcription factor Zfp57 recognizes the methylated CpG within the TGCCGC element. We determined the structure of the DNA-binding domain of Zfp57, consisting of two adjacent zinc fingers, in complex with fully methylated DNA at 1.0 Å resolution. The first zinc finger contacts the 5' half (TGC), and the second recognizes the 3' half (CGC) of the recognition sequence. Zfp57 recognizes the two 5-methylcytosines (5mCs) asymmetrically: One involves hydrophobic interactions with Arg178, which also interacts with the neighboring 3' guanine and forms a 5mC-Arg-G interaction, while the other involves a layer of ordered water molecules. Two point mutations in patients with transient neonatal diabetes abolish DNA-binding activity. Zfp57 has reduced binding affinity for unmodified DNA and the oxidative products of 5mC.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, 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: 14.25 kDa 
• Atom Count: 1,393 
• Modeled Residue Count: 81 
• Deposited Residue Count: 82 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein 57	C	60	Mus musculus	Mutation(s): 0  Gene Names: Zfp57
UniProt
Find proteins for Q8C6P8 (Mus musculus) Explore Q8C6P8  Go to UniProtKB:  Q8C6P8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3')	A	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*TP*GP*(5CM)P*GP*GP*CP*AP*AP*T)-3')	B	11	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	E [auth C], F [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	G [auth C], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	I [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free:  0.140 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.131 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.218	α = 90
b = 60.641	β = 90
c = 96.119	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: 2012-10-17 
Deposition Author(s): Liu, Y., Zhang, X., Cheng, X.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations