5L0M

hLRH-1 DNA Binding Domain - 12bp Oct4 promoter complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).

Weikum, E.R.Tuntland, M.L.Murphy, M.N.Ortlund, E.A.

(2016) J Mol Biol 428: 4981-4992

  • DOI: 10.1016/j.jmb.2016.10.025
  • Primary Citation of Related Structures:  
    5KRB, 5L0M

  • PubMed Abstract: 
  • Oct4 is a transcription factor required for maintaining pluripotency and self-renewal in stem cells. Prior to differentiation, Oct4 must be silenced to allow for the development of the three germ layers in the developing embryo. This fine-tuning is controlled by the nuclear receptors (NRs), liver receptor homolog-1 (LRH-1) and germ cell nuclear factor (GCNF) ...

    Oct4 is a transcription factor required for maintaining pluripotency and self-renewal in stem cells. Prior to differentiation, Oct4 must be silenced to allow for the development of the three germ layers in the developing embryo. This fine-tuning is controlled by the nuclear receptors (NRs), liver receptor homolog-1 (LRH-1) and germ cell nuclear factor (GCNF). Liver receptor homolog-1 is responsible for driving the expression of Oct4 where GCNF represses its expression upon differentiation. Both receptors bind to a DR0 motif located within the Oct4 promoter. Here, we present the first structure of mouse GCNF DNA-binding domain in complex with the Oct4 DR0. The overall structure revealed two molecules bound in a head-to-tail fashion on opposite sides of the DNA. Additionally, we solved the structure of the human LRH-1 DNA-binding domain bound to the same element. We explore the structural elements that govern Oct4 recognition by these two NRs.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322 USA. Electronic address: eortlun@emory.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 5 group A member 2 A112Homo sapiensMutation(s): 0 
Gene Names: NR5A2B1FCPFFTF
Find proteins for O00482 (Homo sapiens)
Explore O00482 
Go to UniProtKB:  O00482
NIH Common Fund Data Resources
PHAROS:  O00482
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3')C12Mus musculus
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3')B12Mus musculus
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      C
      GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      A
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.20 Å
      • R-Value Free: 0.197 
      • R-Value Work: 0.153 
      • R-Value Observed: 0.158 
      • Space Group: P 43
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 40.931α = 90
      b = 40.931β = 90
      c = 105.055γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United States4R01DK095750-05

      Revision History  (Full details and data files)

      • Version 1.0: 2016-11-09
        Type: Initial release
      • Version 1.1: 2017-01-04
        Changes: Database references
      • Version 1.2: 2017-04-05
        Changes: Database references
      • Version 1.3: 2017-09-20
        Changes: Author supporting evidence
      • Version 1.4: 2019-12-25
        Changes: Author supporting evidence