6AKP | pdb_00006akp

Crystal Structural of FOXC2 DNA binding domain bound to PC promoter

• PDB DOI: https://doi.org/10.2210/pdb6AKP/pdb
• NAKB: 6AKP

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


• Deposited: 2018-09-03 Released: 2019-02-06 
• Deposition Author(s): Chen, X., Wei, H., Li, J., Liang, X., Dai, S., Jiang, L., Guo, M., Chen, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structural basis for DNA recognition by FOXC2.

Chen, X., Wei, H., Li, J., Liang, X., Dai, S., Jiang, L., Guo, M., Qu, L., Chen, Z., Chen, L., Chen, Y.

(2019) Nucleic Acids Res 47: 3752-3764

• PubMed: 30722065 
• DOI: https://doi.org/10.1093/nar/gkz077
• Primary Citation Related Structures: 
  6AKO, 6AKP


• PubMed Abstract: 
  

  The FOXC family of transcription factors (FOXC1 and FOXC2) plays essential roles in the regulation of embryonic, ocular, and cardiac development. Mutations and abnormal expression of FOXC proteins are implicated in genetic diseases as well as cancer. In this study, we determined two crystal structures of the DNA-binding domain (DBD) of human FOXC2 protein, in complex with different DNA sites. The FOXC2-DBD adopts the winged-helix fold with helix H3 contributing to all the base specific contacts, while the N-terminus, wing 1, and the C-terminus of FOXC2-DBD all make additional contacts with the phosphate groups of DNA. Our structural, biochemical, and bioinformatics analyses allow us to revise the previously proposed DNA recognition mechanism and provide a model of DNA binding for the FOXC proteins. In addition, our structural analysis and accompanying biochemical assays provide a molecular basis for understanding disease-causing mutations in FOXC1 and FOXC2.

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Organizational Affiliation: 
• NHC Key Laboratory of Cancer Proteomics and Laboratory of Structural Biology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
Key Laboratory of Medical Genetics and College of Life Science, Central South University, Changsha, Hunan 410008, China.
Molecular and Computational Biology Program, Department of Biological Sciences and Department of Chemistry, University of Southern California, Los Angeles, CA 90089, 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: 22.15 kDa 
• Atom Count: 1,464 
• Modeled Residue Count: 126 
• Deposited Residue Count: 135 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Forkhead box protein C2	C	103	Homo sapiens	Mutation(s): 0  Gene Names: FOXC2, FKHL14, MFH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99958 (Homo sapiens) Explore Q99958  Go to UniProtKB:  Q99958
PHAROS:  Q99958 GTEx:  ENSG00000176692

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(AP*CP*AP*CP*AP*AP*AP*TP*AP*TP*TP*TP*GP*TP*GP*T)-3')	A, B	16	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.837	α = 90
b = 80.214	β = 90
c = 101.154	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
HKL-3000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Chen, X., Wei, H., Li, J., Liang, X., Dai, S., Jiang, L., Guo, M., Chen, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81372904
National Natural Science Foundation of China	China	81570537

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 1.1: 2019-02-13
  Changes: Data collection, Database references
• Version 1.2: 2019-05-01
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description