2WTY | pdb_00002wty

Crystal structure of the homodimeric MafB in complex with the T-MARE binding site

• PDB DOI: https://doi.org/10.2210/pdb2WTY/pdb
• NAKB: 2WTY

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-09-25 Released: 2010-12-08 
• Deposition Author(s): Consani Textor, L., Holton, S., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.275 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Design of a bZIP Transcription Factor with Homo/Heterodimer-Induced DNA-Binding Preference.

Pogenberg, V., Consani Textor, L., Vanhille, L., Holton, S.J., Sieweke, M.H., Wilmanns, M.

(2014) Structure 22: 466

• PubMed: 24530283 
• DOI: https://doi.org/10.1016/j.str.2013.12.017
• Primary Citation Related Structures: 
  2WT7, 2WTY


• PubMed Abstract: 
  

  The ability of basic leucine zipper transcription factors for homo- or heterodimerization provides a paradigm for combinatorial control of eukaryotic gene expression. It has been unclear, however, how facultative dimerization results in alternative DNA-binding repertoires on distinct regulatory elements. To unravel the molecular basis of such coupled preferences, we determined two high-resolution structures of the transcription factor MafB as a homodimer and as a heterodimer with c-Fos bound to variants of the Maf-recognition element. The structures revealed several unexpected and dimer-specific coiled-coil-heptad interactions. Based on these findings, we have engineered two MafB mutants with opposite dimerization preferences. One of them showed a strong preference for MafB/c-Fos heterodimerization and enabled selection of heterodimer-favoring over homodimer-specific Maf-recognition element variants. Our data provide a concept for transcription factor design to selectively activate dimer-specific pathways and binding repertoires.

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Organizational Affiliation: 
• EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany.
Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille Université, UM2, Campus de Luminy, Case 906, 13288 Marseille Cedex 09, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France; Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France.
Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille Université, UM2, Campus de Luminy, Case 906, 13288 Marseille Cedex 09, France; Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France; Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France; Max-Delbrück-Centrum für Molekulare Medizin (MDC), Robert-Rössle-Straße 10, 13125 Berlin, Germany.
EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.68 kDa 
• Atom Count: 2,459 
• Modeled Residue Count: 230 
• Deposited Residue Count: 234 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTION FACTOR MAFB	A, B	97	Mus musculus	Mutation(s): 2
UniProt
Find proteins for P54841 (Mus musculus) Explore P54841  Go to UniProtKB:  P54841

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*AP*TP*TP*GP*CP*TP*GP*AP*CP*TP*CP*AP *GP*CP*AP*AP*AP*T)-3')	C	20	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*TP*TP*TP*GP*CP*TP*GP*AP*GP*TP*CP*AP *GP*CP*AP*AP*TP*T)-3')	D	20	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.275 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.15	α = 90
b = 49.82	β = 90
c = 170.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Consani Textor, L., Holton, S., Wilmanns, M.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references, Source and taxonomy, Version format compliance
• Version 1.2: 2014-03-19
  Changes: Database references
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other