5VPF

Transcription factor FosB/JunD bZIP domain in complex with cognate DNA, type-II crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Activator Protein-1: redox switch controlling structure and DNA-binding.

Yin, Z.Machius, M.Nestler, E.J.Rudenko, G.

(2017) Nucleic Acids Res 45: 11425-11436

  • DOI: 10.1093/nar/gkx795
  • Primary Citation of Related Structures:  
    5VPB, 5VPA, 5VPD, 5VPC, 5VPF, 5VPE

  • PubMed Abstract: 
  • The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA ...

    The transcription factor, activator protein-1 (AP-1), binds to cognate DNA under redox control; yet, the underlying mechanism has remained enigmatic. A series of crystal structures of the AP-1 FosB/JunD bZIP domains reveal ordered DNA-binding regions in both FosB and JunD even in absence DNA. However, while JunD is competent to bind DNA, the FosB bZIP domain must undergo a large conformational rearrangement that is controlled by a 'redox switch' centered on an inter-molecular disulfide bond. Solution studies confirm that FosB/JunD cannot undergo structural transition and bind DNA when the redox-switch is in the 'OFF' state, and show that the mid-point redox potential of the redox switch affords it sensitivity to cellular redox homeostasis. The molecular and structural studies presented here thus reveal the mechanism underlying redox-regulation of AP-1 Fos/Jun transcription factors and provide structural insight for therapeutic interventions targeting AP-1 proteins.


    Organizational Affiliation

    Department of Pharmacology and Toxicology, and the Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein fosBA, E [auth C]68Homo sapiensMutation(s): 0 
Gene Names: FOSBG0S3
UniProt & NIH Common Fund Data Resources
Find proteins for P53539 (Homo sapiens)
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Go to UniProtKB:  P53539
PHAROS:  P53539
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor jun-DB, F [auth D]68Homo sapiensMutation(s): 0 
Gene Names: JUND
UniProt & NIH Common Fund Data Resources
Find proteins for P17535 (Homo sapiens)
Explore P17535 
Go to UniProtKB:  P17535
PHAROS:  P17535
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*CP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')C [auth E], G19Homo sapiens
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*TP*CP*GP*GP*TP*GP*AP*GP*TP*CP*AP*CP*CP*GP*AP*CP*G)-3')D [auth F], H19Homo sapiens
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PO4
      Query on PO4

      Download Ideal Coordinates CCD File 
      S [auth C], U [auth G]PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       Ligand Interaction
      EDO
      Query on EDO

      Download Ideal Coordinates CCD File 
      I [auth A], J [auth A], K [auth A], M [auth B], P [auth E], Q [auth F], R [auth C], T [auth D]1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      CL
      Query on CL

      Download Ideal Coordinates CCD File 
      L [auth A], N [auth B]CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      NA
      Query on NA

      Download Ideal Coordinates CCD File 
      O [auth B]SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.69 Å
      • R-Value Free: 0.248 
      • R-Value Work: 0.210 
      • R-Value Observed: 0.213 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 119.637α = 90
      b = 119.637β = 90
      c = 249.97γ = 120
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      SCALEPACKdata scaling
      PDB_EXTRACTdata extraction
      DENZOdata reduction
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01 DA040621
      Brain and Behavior Research FoundationUnited States--

      Revision History  (Full details and data files)

      • Version 1.0: 2017-09-06
        Type: Initial release
      • Version 1.1: 2017-10-18
        Changes: Database references
      • Version 1.2: 2017-11-15
        Changes: Database references
      • Version 1.3: 2019-12-11
        Changes: Author supporting evidence