5KRB

GCNF DNA Binding Domain - Oct4 DR0 Complex

  • Classification: transcription/dna
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli BL21
  • Mutation(s): Yes 

  • Deposited: 2016-07-07 Released: 2016-11-09 
  • Deposition Author(s): Weikum, E.R., Ortlund, E.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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:  
    5L0M, 5KRB

  • 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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 6 group A member 1B, D [auth G]84Mus musculusMutation(s): 1 
Gene Names: Nr6a1Gcnf
UniProt & NIH Common Fund Data Resources
Find proteins for Q64249 (Mus musculus)
Explore Q64249 
Go to UniProtKB:  Q64249
IMPC:  MGI:1352459
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)-3')A16Mus musculus
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)-3')C [auth E]16Mus musculus
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.10 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.216 
      • R-Value Observed: 0.218 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 53.649α = 90
      b = 69.469β = 90
      c = 84.536γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data scaling
      PDB_EXTRACTdata extraction
      PHASERphasing
      Cootmodel building
      HKL-2000data reduction

      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 States1R01DK095750-01
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1F31GM113397-01A1

      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