3F5C | pdb_00003f5c

Structure of Dax-1:LRH-1 complex

• PDB DOI: https://doi.org/10.2210/pdb3F5C/pdb

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


• Deposited: 2008-11-03 Released: 2008-12-23 
• Deposition Author(s): Fletterick, R.J., Sablin, E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.279 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

The structure of corepressor Dax-1 bound to its target nuclear receptor LRH-1.

Sablin, E.P., Woods, A., Krylova, I.N., Hwang, P., Ingraham, H.A., Fletterick, R.J.

(2008) Proc Natl Acad Sci U S A 105: 18390-18395

• PubMed: 19015525 
• DOI: https://doi.org/10.1073/pnas.0808936105
• Primary Citation Related Structures: 
  3F5C


• PubMed Abstract: 
  

  The Dax-1 protein is an enigmatic nuclear receptor that lacks an expected DNA binding domain, yet functions as a potent corepressor of nuclear receptors. Here we report the structure of Dax-1 bound to one of its targets, liver receptor homolog 1 (LRH-1). Unexpectedly, Dax-1 binds to LRH-1 using a new module, a repressor helix built from a family conserved sequence motif, PCFXXLP. Mutations in this repressor helix that are linked with human endocrine disorders dissociate the complex and attenuate Dax-1 function. The structure of the Dax-1:LRH-1 complex provides the molecular mechanism for the function of Dax-1 as a potent transcriptional repressor.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 89.48 kDa 
• Atom Count: 4,936 
• Modeled Residue Count: 607 
• Deposited Residue Count: 784 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 5 group A member 2	A	248	Mus musculus	Mutation(s): 1  Gene Names: Nr5a2, Lrh1
UniProt
Find proteins for P45448 (Mus musculus) Explore P45448  Go to UniProtKB:  P45448

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 0 group B member 1	B, C	268	Mus musculus	Mutation(s): 0  Gene Names: Nr0b1, Ahch, Dax1
UniProt & NIH Common Fund Data Resources
Find proteins for Q61066 (Mus musculus) Explore Q61066  Go to UniProtKB:  Q61066
IMPC:  MGI:1352460

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.279 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.355	α = 90
b = 103.355	β = 90
c = 117.455	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Fletterick, R.J., Sablin, E.P.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description