Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.30 kDa 
• Atom Count: 2464 
• Residue Count: 284 
• Unique protein chains: 2

1ZGY

Structural and Biochemical Basis for Selective Repression of the Orphan Nuclear Receptor LRH-1 by SHP

• DOI: 10.2210/pdb1ZGY/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, Rattus norvegicus
• Mutation(s): No 


• Deposited: 2005-04-22 Released: 2005-07-26 
• Deposition Author(s): Li, Y., Choi, M., Suino, K., Kovach, A., Daugherty, J., Kliewer, S.A., Xu, H.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 

Literature

Structural and biochemical basis for selective repression of the orphan nuclear receptor liver receptor homolog 1 by small heterodimer partner.

Li, Y., Choi, M., Suino, K., Kovach, A., Daugherty, J., Kliewer, S.A., Xu, H.E.

(2005) Proc Natl Acad Sci U S A 102: 9505-9510

• PubMed: 15976031 
• DOI: 10.1073/pnas.0501204102
• Primary Citation of Related Structures:  
  1ZGY, 1ZH7


• PubMed Abstract: 
  

The functional interaction between the orphan nuclear receptors small heterodimer partner (SHP) and liver receptor homolog 1 (LRH-1), where SHP binds to LRH-1 and represses its constitutive transcriptional activity, is crucial for regulating genes involved in cholesterol homeostasis. Here, we report structural and biochemical analyses of the LRH-1/SHP interaction. The crystal structure and modeling studies of the LRH-1 ligand-binding domain bound to either of the two LXXLL-related motifs of SHP show that the receptor undergoes conformational changes to accommodate the SHP docking and reveal key residues that determine the potency and selectivity of SHP binding. Through a combination of mutagenesis and binding studies, we demonstrate that only the second SHP LXXLL motif is required for repressing LRH-1, and this motif displays a strong preference for binding to LRH-1 over the closely related receptor steroidogeneic factor 1 (SF-1). Structural comparisons indicate that this binding selectivity is determined by residues flanking the core LXXLL motifs. These results establish a structural model for understanding how SHP interacts with LRH-1 to regulate cholesterol homeostasis and provide new insights into how nuclear receptor/coregulator selectivity is achieved.

---

Organizational Affiliation: 

Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue, Grand Rapids, MI 49503, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator activated receptor gamma	A	272	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231 GTEx  ENSG00000132170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 0, group B, member 2	B	17	Rattus norvegicus	Mutation(s): 0  Gene Names: Nr0b2, Shp
Find proteins for P97947 (Rattus norvegicus) Explore P97947  Go to UniProtKB:  P97947

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BRL	A	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) C18 H19 N3 O3 S YASAKCUCGLMORW-HNNXBMFYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BRL	IC50:  103   nM  BindingDB
BRL	Ki:  8   nM  BindingDB
BRL	IC50:  112   nM  BindingDB
BRL	EC50:  396   nM  BindingDB
BRL	EC50:  1   nM  BindingDB
BRL	IC50:  159   nM  BindingDB
BRL	EC50:  260   nM  BindingDB
BRL	EC50:  20   nM  BindingDB
BRL	EC50:  316   nM  BindingDB
BRL	EC50:  300   nM  BindingDB
BRL	EC50:  326   nM  BindingDB
BRL	EC50:  332   nM  BindingDB
BRL	EC50:  52   nM  BindingDB
BRL	EC50:  30   nM  BindingDB
BRL	IC50:  292   nM  BindingDB
BRL	IC50:  298   nM  BindingDB
BRL	Ki:  27   nM  BindingDB
BRL	EC50:  39   nM  BindingDB
BRL	EC50:  40   nM  BindingDB
BRL	IC50:  1   nM  BindingDB
BRL	EC50:  95   nM  BindingDB
BRL	EC50:  89   nM  BindingDB
BRL	EC50:  100   nM  BindingDB
BRL	EC50:  1600   nM  BindingDB
BRL	EC50:  117   nM  BindingDB
BRL	EC50:  120   nM  BindingDB
BRL	EC50:  114   nM  BindingDB
BRL	Kd:  0.14000000059604645   nM  BindingDB
BRL	EC50:  4   nM  BindingDB
BRL	Ki:  47   nM  BindingDB
BRL	EC50:  1100   nM  BindingDB
BRL	IC50:  38   nM  BindingDB
BRL	Kd:  1.2000000476837158   nM  BindingDB
BRL	EC50:  87   nM  BindingDB
BRL	EC50:  83   nM  BindingDB
BRL	IC50:  500   nM  Binding MOAD
BRL	EC50:  240   nM  BindingDB
BRL	EC50:  8   nM  BindingDB
BRL	IC50:  76   nM  BindingDB
BRL	EC50:  10   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.231 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.602	α = 90
b = 54.493	β = 97.5
c = 66.497	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-22 
• Released Date: 2005-07-26 
Deposition Author(s): Li, Y., Choi, M., Suino, K., Kovach, A., Daugherty, J., Kliewer, S.A., Xu, H.E.

Revision History 

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description