6NCE image
Deposition Date 2018-12-11
Release Date 2019-02-27
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6NCE
Keywords:
DNA BINDING PROTEIN/DNA
Title:
Crystal structure of the human FOXN3 DNA binding domain in complex with a forkhead DNA sequence
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.60 Å
R-Value Free:
0.27
R-Value Work:
0.23
Space Group:
C 1 2 1
6NCE validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Forkhead box protein N3
Gene (Uniprot):FOXN3
Chain IDs:A
Chain Length:100
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O00409 Pfam ID:PF00250
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*CP*TP*TP*AP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3')
Chain IDs:B (auth: C)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*AP*CP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*TP*AP*AP*G)-3')
Chain IDs:C (auth: D)
Chain Length:16
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
GOL
MG
Primary Citation
Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes.
Mol. Cell 74 245 ? (2019)
PMID: 30826165 DOI: 10.1016/j.molcel.2019.01.019

Abstact

Transcription factors (TFs) control gene expression by binding DNA recognition sites in genomic regulatory regions. Although most forkhead TFs recognize a canonical forkhead (FKH) motif, RYAAAYA, some forkheads recognize a completely different (FHL) motif, GACGC. Bispecific forkhead proteins recognize both motifs, but the molecular basis for bispecific DNA recognition is not understood. We present co-crystal structures of the FoxN3 DNA binding domain bound to the FKH and FHL sites, respectively. FoxN3 adopts a similar conformation to recognize both motifs, making contacts with different DNA bases using the same amino acids. However, the DNA structure is different in the two complexes. These structures reveal how a single TF binds two unrelated DNA sequences and the importance of DNA shape in the mechanism of bispecific recognition.

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Primary Citation of related structures
6NCE