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: 20.27 kDa 
• Atom Count: 1389 
• Residue Count: 111 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3L2C

Crystal Structure of the DNA Binding Domain of FOXO4 Bound to DNA

• DOI: 10.2210/pdb3L2C/pdb
• Entry: 3L2C supersedes: 3BPY
• NDB: NA0394

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-15 Released: 2009-12-29 
• Deposition Author(s): Boura, E., Silhan, J., Sulc, M., Brynda, J., Obsilova, V., Obsil, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structure of the human FOXO4-DBD-DNA complex at 1.9 A resolution reveals new details of FOXO binding to the DNA

Boura, E., Rezabkova, L., Brynda, J., Obsilova, V., Obsil, T.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1351-1357

• PubMed: 21123876 
• DOI: 10.1107/S0907444910042228
• Primary Citation of Related Structures:  
  3L2C


• PubMed Abstract: 
  

FOXO4 is a member of the FOXO subgroup of forkhead transcription factors that constitute key components of a conserved signalling pathway that connects growth and stress signals to transcriptional control. Here, the 1.9 Å resolution crystal structure of the DNA-binding domain of human FOXO4 (FOXO4-DBD) bound to a 13 bp DNA duplex containing a FOXO consensus binding sequence is reported. The structure shows a similar recognition of the core sequence as has been shown for two other FOXO proteins. Helix H3 is docked into the major groove and provides all of the base-specific contacts, while the N-terminus and wing W1 make additional contacts with the phosphate groups of DNA. In contrast to other FOXO-DBD-DNA structures, the loop between helices H2 and H3 has a different conformation and participates in DNA binding. In addition, the structure of the FOXO4-DBD-DNA complex suggests that both direct water-DNA base contacts and the unique water-network interactions contribute to FOXO-DBD binding to the DNA in a sequence-specific manner.

---

Organizational Affiliation: 

Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Forkhead box protein O4	A	110	Homo sapiens	Mutation(s): 0  Gene Names: AFX, AFX1, FOXO4, MLLT7
Find proteins for P98177 (Homo sapiens) Explore P98177  Go to UniProtKB:  P98177
NIH Common Fund Data Resources
PHAROS:  P98177 GTEx:  ENSG00000184481

Entity ID: 1
Molecule	Chains	Length	Organism	Image
FOXO consensus binding sequence, plus strand	B	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
FOXO consensus binding sequence, minus strand	C	13	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.228 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.81	α = 90
b = 71.7	β = 90
c = 131.86	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-15 
• Released Date: 2009-12-29 
Deposition Author(s): Boura, E., Silhan, J., Sulc, M., Brynda, J., Obsilova, V., Obsil, T.
• This entry supersedes: 3BPY

Revision History 

• Version 1.0: 2009-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance