Macromolecule Content

• Total Structure Weight: 19.39 kDa 
• Atom Count: 1307 
• Modelled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2KMK

Gfi-1 Zinc Fingers 3-5 complexed with DNA

• DOI: 10.2210/pdb2KMK/pdb
• NDB: 2KMK

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-30 Released: 2010-03-02 
• Deposition Author(s): Lee, S., Wu, Z.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of Gfi-1 zinc domain bound to consensus DNA.

Lee, S., Doddapaneni, K., Hogue, A., McGhee, L., Meyers, S., Wu, Z.

(2010) J Mol Biol 397: 1055-1066

• PubMed: 20153336 
• DOI: 10.1016/j.jmb.2010.02.006
• Primary Citation of Related Structures:  
  2KMK


• PubMed Abstract: 
  

Gfi-1 is a crucial transcriptional repressor for the precise regulation of cell proliferation and differentiation in hematopoiesis. Recently, this protein has also been demonstrated to be capable of restricting the proliferation of hematopoietic stem cells, a process that appears to be vital for the long-term competency of hematopoietic stem cells. These two seemingly opposite outcomes of regulation are likely to arise from its interactions with a variety of cellular partners. Such interactions can directly affect the genes that Gfi-1 recognizes through its DNA binding zinc-finger domain. In this work, we report the determination of the solution structure of Gfi-1 zinc fingers 3-5 in complex with a 16-mer consensus DNA using multidimensional NMR method. Unlike a proposed minor-groove binding model based on methylation interference experiments, our structure clearly shows that Gfi-1 zinc fingers 3-5 bind into the major groove of the target DNA reminiscent of canonical C(2)H(2) zinc-finger domains. The fourth and fifth zinc fingers recognize the AATC core sequence by forming base-specific hydrogen bonds between the side chains of Asn382, Gln379, and Asp354 and the bases of the invariant adenines and cytosine. Overall, the current work provides valuable insight into the structural determinants for DNA binding specificity, in particular for the TCA triplet that has not been observed in any other structures of zinc finger-DNA complexes, as well as molecular rationales for a naturally occurring mutation that causes acute myeloid leukemia.

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Organizational Affiliation: 

Biochemistry Department, Ohio State University, Columbus, OH 43210, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein Gfi-1	A	82	Rattus norvegicus	Mutation(s): 0  Gene Names: Gfi1, Gfi-1
Find proteins for Q07120 (Rattus norvegicus) Explore Q07120  Go to UniProtKB:  Q07120

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP*TP*GP*CP*CP*TP*A)-3')	B	16	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*CP*AP*GP*TP*GP*AP*TP*TP*TP*AP*TP*G)-3')	C	16	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KMK Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-30 
• Released Date: 2010-03-02 
Deposition Author(s): Lee, S., Wu, Z.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance