1OT7 | pdb_00001ot7

Structural Basis for 3-deoxy-CDCA Binding and Activation of FXR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.279 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural Basis for Bile Acid Binding and Activation of the Nuclear Receptor FXR

Mi, L.Z.Devarakonda, S.Harp, J.M.Han, Q.Pellicciari, R.Willson, T.M.Khorasanizadeh, S.Rastinejad, F.

(2003) Mol Cell 11: 1093-1100

  • DOI: https://doi.org/10.1016/s1097-2765(03)00112-6
  • Primary Citation Related Structures: 
    1OSV, 1OT7

  • PubMed Abstract: 

    The nuclear receptor FXR is the sensor of physiological levels of enterohepatic bile acids, the end products of cholesterol catabolism. Here we report crystal structures of the FXR ligand binding domain in complex with coactivator peptide and two different bile acids. An unusual A/B ring juncture, a feature associated with bile acids and no other steroids, provides ligand discrimination and triggers a pi-cation switch that activates FXR. Helix 12, the activation function 2 of the receptor, adopts the agonist conformation and stabilizes coactivator peptide binding. FXR is able to interact simultaneously with two coactivator motifs, providing a mechanism for enhanced binding of coactivators through intermolecular contacts between their LXXLL sequences. These FXR complexes provide direct insights into the design of therapeutic bile acids for treatment of hyperlipidemia and cholestasis.


  • Organizational Affiliation
    • Department of Pharmacology, University of Virginia Health System, Charlottesville 22908, USA.

Macromolecule Content 

  • Total Structure Weight: 58.71 kDa 
  • Atom Count: 4,140 
  • Modeled Residue Count: 494 
  • Deposited Residue Count: 494 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bile Acid Receptor
A, B
229Rattus norvegicusMutation(s): 0 
Gene Names: NR1H4
UniProt
Find proteins for Q62735 (Rattus norvegicus)
Explore Q62735 
Go to UniProtKB:  Q62735
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62735
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
dodecamer peptide fragment of RPGR-interacting protein 1
C, D, E
12N/AMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHC

Query on CHC



Download:Ideal Coordinates CCD File
F [auth A]6-ETHYL-CHENODEOXYCHOLIC ACID
C26 H44 O4
ZXERDUOLZKYMJM-ZWECCWDJSA-N
IU5

Query on IU5



Download:Ideal Coordinates CCD File
G [auth B]ISO-URSODEOXYCHOLIC ACID
C24 H40 O4
RUDATBOHQWOJDD-DNMBCGTGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.279 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.536α = 90
b = 107.129β = 90
c = 69.203γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description