Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 15.08 kDa 
• Atom Count: 1148 
• Residue Count: 101 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2WBS

Crystal structure of the zinc finger domain of Klf4 bound to its target DNA

• DOI: 10.2210/pdb2WBS/pdb
• NDB: NA0486

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


• Deposited: 2009-03-03 Released: 2010-04-07 
• Deposition Author(s): Zocher, G., Schuetz, A., Carstanjen, D., Heinemann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

The Structure of the Klf4 DNA-Binding Domain Links to Self-Renewal and Macrophage Differentiation.

Schuetz, A., Nana, D., Rose, C., Zocher, G., Milanovic, M., Koenigsmann, J., Blasig, R., Heinemann, U., Carstanjen, D.

(2011) Cell Mol Life Sci 68: 3121

• PubMed: 21290164 
• DOI: 10.1007/s00018-010-0618-x
• Primary Citation of Related Structures:  
  2WBU, 2WBS


• PubMed Abstract: 
  

Krueppel-like factor 4 (Klf4) belongs to the Sp/Klf family of zinc-finger transcription factors and is indispensable for terminal maturation of epithelial tissues. Furthermore, it is part of a small set of proteins that are used to generate pluripotent embryonic stem cells from differentiated tissues. Herein, we describe that a Klf4 zinc-finger domain mutant induces self-renewal and block of maturation, while wild-type Klf4 induces terminal macrophage differentiation. Moreover, we present the crystal structure of the zinc-finger domain of Klf4 bound to its target DNA, revealing that primarily the two C-terminal zinc-finger motifs are required for site specificity. Lack of those two zinc fingers leads to deficiency of Klf4 to induce macrophage differentiation. The first zinc finger, on the other hand, inhibits the otherwise cryptic self-renewal and block of differentiation activity of Klf4. Our data show that impairing the DNA binding could potentially contribute to a monocytic leukemia.

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Organizational Affiliation: 

Protein Sample Production Facility, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KRUEPPEL-LIKE FACTOR 4	A	89	Mus musculus	Mutation(s): 0  Gene Names: Klf4, Ezf, Gklf, Zie
Find proteins for Q60793 (Mus musculus) Explore Q60793  Go to UniProtKB:  Q60793
NIH Common Fund Data Resources
IMPC  MGI:1342287

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*GP*GP*CP*GP*CP)-3'	F	7	Mus musculus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*CP*CP*TP*CP)-3'	G	7	Mus musculus

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.232 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41	α = 90
b = 45.97	β = 90
c = 73.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-03 
• Released Date: 2010-04-07 
Deposition Author(s): Zocher, G., Schuetz, A., Carstanjen, D., Heinemann, U.

Revision History 

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-10-05
  Changes: Database references, Source and taxonomy