Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.27 kDa 
• Atom Count: 294 
• Modelled Residue Count: 37 
• Deposited Residue Count: 37 
• Unique protein chains: 1

1P7A

Solution Structure of the Third Zinc Finger from BKLF

• PDB DOI: 10.2210/pdb1P7A/pdb
• BMRB: 5851

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-04-30 Released: 2003-12-30 
• Deposition Author(s): Simpson, R.J.Y., Cram, E.D., Czolij, R., Matthews, J.M., Crossley, M., Mackay, J.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 35 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.

Simpson, R.J., Cram, E.D., Czolij, R., Matthews, J.M., Crossley, M., Mackay, J.P.

(2003) J Biol Chem 278: 28011-28018

• PubMed: 12736264 
• DOI: 10.1074/jbc.M211146200
• Primary Citation of Related Structures:  
  1P7A


• PubMed Abstract: 
  

Classical (CCHH) zinc fingers are among the most common protein domains found in eukaryotes. They function as molecular recognition elements that mediate specific contact with DNA, RNA, or other proteins and are composed of a betabetaalpha fold surrounding a single zinc ion that is ligated by two cysteine and two histidine residues. In a number of variant zinc fingers, the final histidine is not conserved, and in other unrelated zinc binding domains, residues such as aspartate can function as zinc ligands. To test whether the final histidine is required for normal folding and the DNA-binding function of classical zinc fingers, we focused on finger 3 of basic Krüppel-like factor. The structure of this domain was determined using NMR spectroscopy and found to constitute a typical classical zinc finger. We generated a panel of substitution mutants at the final histidine in this finger and found that several of the mutants retained some ability to fold in the presence of zinc. Consistent with this result, we showed that mutation of the final histidine had only a modest effect on DNA binding in the context of the full three-finger DNA-binding domain of basic Krüppel-like factor. Further, the zinc binding ability of one of the point mutants was tested and found to be indistinguishable from the wild-type domain. These results suggest that the final zinc chelating histidine is not an essential feature of classical zinc fingers and have implications for zinc finger evolution, regulation, and the design of experiments testing the functional roles of these domains.

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Organizational Affiliation: 

School of Molecular and Microbial Biosciences, G08, University of Sydney, New South Wales 2006, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kruppel-like factor 3	A	37	Mus musculus	Mutation(s): 0  Gene Names: Bklf, Klf3
UniProt
Find proteins for Q60980 (Mus musculus) Explore Q60980  Go to UniProtKB:  Q60980

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 35 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1P7A Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-30 
• Released Date: 2003-12-30 
Deposition Author(s): Simpson, R.J.Y., Cram, E.D., Czolij, R., Matthews, J.M., Crossley, M., Mackay, J.P.

Revision History  

• Version 1.0: 2003-12-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-12-28
  Changes: Structure summary