Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 34.81 kDa 
• Atom Count: 2168 
• Residue Count: 222 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

4EOT

Crystal structure of the MafA homodimer bound to the consensus MARE

• DOI: 10.2210/pdb4EOT/pdb
• NDB: NA1736

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


• Deposited: 2012-04-15 Released: 2012-11-28 
• Deposition Author(s): Lu, X., Guanga, G., Wan, C., Rose, R.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.260 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

A Novel DNA Binding Mechanism for maf Basic Region-Leucine Zipper Factors Inferred from a MafA-DNA Complex Structure and Binding Specificities.

Lu, X., Guanga, G.P., Wan, C., Rose, R.B.

(2012) Biochemistry 51: 9706-9717

• PubMed: 23148532 
• DOI: 10.1021/bi301248j
• Structures With Same Primary Citation


• PubMed Abstract: 
  

MafA is a proto-oncoprotein and is critical for insulin gene expression in pancreatic β-cells. Maf proteins belong to the AP1 superfamily of basic region-leucine zipper (bZIP) transcription factors. Residues in the basic helix and an ancillary N-terminal domain, the Extended Homology Region (EHR), endow maf proteins with unique DNA binding properties: binding a 13 bp consensus site consisting of a core AP1 site (TGACTCA) flanked by TGC sequences and binding DNA stably as monomers. To further characterize maf DNA binding, we determined the structure of a MafA-DNA complex. MafA forms base-specific hydrogen bonds with the flanking G(-5)C(-4) and central C(0)/G(0) bases, but not with the core-TGA bases. However, in vitro binding studies utilizing a pulse-chase electrophoretic mobility shift assay protocol revealed that mutating either the core-TGA or flanking-TGC bases dramatically increases the binding off rate. Comparing the known maf structures, we propose that DNA binding specificity results from positioning the basic helix through unique phosphate contacts. The EHR does not contact DNA directly but stabilizes DNA binding by contacting the basic helix. Collectively, these results suggest a novel multistep DNA binding process involving a conformational change from contacting the core-TGA to contacting the flanking-TGC bases.

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Organizational Affiliation: 

Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Transcription factor MafA	A, B	95	Homo sapiens	Mutation(s): 0  Gene Names: MAFA
Find proteins for Q8NHW3 (Homo sapiens) Explore Q8NHW3  Go to UniProtKB:  Q8NHW3
NIH Common Fund Data Resources
PHAROS  Q8NHW3 GTEx  ENSG00000182759

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*CP*CP*GP*GP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP*GP*CP*AP*GP*G)-3'	C	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP*GP*CP*AP*CP*CP*G)-3'	D	19	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.260 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.1	α = 90
b = 116.1	β = 90
c = 85.08	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-15 
• Released Date: 2012-11-28 
Deposition Author(s): Lu, X., Guanga, G., Wan, C., Rose, R.B.

Revision History 

• Version 1.0: 2012-11-28
  Type: Initial release
  
• Version 1.1: 2012-12-26
  Changes: Database references