2WT7 | pdb_00002wt7

Crystal structure of the bZIP heterodimeric complex MafB:cFos bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.256 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2WT7

This is version 1.5 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • EMBL Hamburg c/o DESY, Notkestraße 85, 22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 28.33 kDa 
  • Atom Count: 2,156 
  • Modeled Residue Count: 185 
  • Deposited Residue Count: 185 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTO-ONCOGENE PROTEIN C-FOS63Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01101 (Mus musculus)
Explore P01101 
Go to UniProtKB:  P01101
IMPC:  MGI:95574
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01101
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TRANSCRIPTION FACTOR MAFB90Mus musculusMutation(s): 1 
UniProt
Find proteins for P54841 (Mus musculus)
Explore P54841 
Go to UniProtKB:  P54841
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54841
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
MODIFIED T-MARE MOTIF16synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
MODIFIED T-MARE MOTIF16synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.256 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.676α = 90
b = 146.676β = 90
c = 51.117γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Source and taxonomy, Version format compliance
  • Version 1.2: 2014-02-26
    Changes: Database references
  • Version 1.3: 2014-03-19
    Changes: Database references
  • Version 1.4: 2019-07-17
    Changes: Data collection
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other