6HL1

Crystal Structure of Farnesoid X receptor (FXR) with bound NCoA-2 peptide and CDCA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4QE6


Literature

Molecular tuning of farnesoid X receptor partial agonism.

Merk, D.Sreeramulu, S.Kudlinzki, D.Saxena, K.Linhard, V.Gande, S.L.Hiller, F.Lamers, C.Nilsson, E.Aagaard, A.Wissler, L.Dekker, N.Bamberg, K.Schubert-Zsilavecz, M.Schwalbe, H.

(2019) Nat Commun 10: 2915-2915

  • DOI: 10.1038/s41467-019-10853-2
  • Primary Citation of Related Structures:  
    6HL0, 6HL1

  • PubMed Abstract: 
  • The bile acid-sensing transcription factor farnesoid X receptor (FXR) regulates multiple metabolic processes. Modulation of FXR is desired to overcome several metabolic pathologies but pharmacological administration of full FXR agonists has been plagued by mechanism-based side effects ...

    The bile acid-sensing transcription factor farnesoid X receptor (FXR) regulates multiple metabolic processes. Modulation of FXR is desired to overcome several metabolic pathologies but pharmacological administration of full FXR agonists has been plagued by mechanism-based side effects. We have developed a modulator that partially activates FXR in vitro and in mice. Here we report the elucidation of the molecular mechanism that drives partial FXR activation by crystallography- and NMR-based structural biology. Natural and synthetic FXR agonists stabilize formation of an extended helix α11 and the α11-α12 loop upon binding. This strengthens a network of hydrogen bonds, repositions helix α12 and enables co-activator recruitment. Partial agonism in contrast is conferred by a kink in helix α11 that destabilizes the α11-α12 loop, a critical determinant for helix α12 orientation. Thereby, the synthetic partial agonist induces conformational states, capable of recruiting both co-repressors and co-activators leading to an equilibrium of co-activator and co-repressor binding.


    Organizational Affiliation

    German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany. schwalbe@em.uni-frankfurt.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bile acid receptorA232Homo sapiensMutation(s): 0 
Gene Names: NR1H4BARFXRHRR1RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens)
Explore Q96RI1 
Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RI1
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NCoA-2 peptide (Nuclear receptor coactivator 2), LYS-GLU-ASN-ALA-LEU-LEU-ARG-TYR-LEU-LEU-ASP-LYS-ASPB13Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JN3
Query on JN3

Download Ideal Coordinates CCD File 
C [auth A]CHENODEOXYCHOLIC ACID
C24 H40 O4
RUDATBOHQWOJDD-BSWAIDMHSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JN3 BindingDB:  6HL1 EC50: min: 1000, max: 3.00e+4 (nM) from 18 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.444α = 90
b = 33.815β = 101.47
c = 83.04γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references