7JYD | pdb_00007jyd

Human Liver Receptor Homolog-1 in Complex with 10CA and a Fragment of Tif2

• PDB DOI: https://doi.org/10.2210/pdb7JYD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-30 Released: 2022-03-02 
• Deposition Author(s): D'Agostino, E.H., Mays, S.G., Ortlund, E.A.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), United States Department of Agriculture (USDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Tapping into a phospholipid-LRH-1 axis yields a powerful anti-inflammatory agent with in vivo activity against colitis

D'Agostino, E.H., Mays, S.G., Flynn, A.F., Huang, X., Wang, G., Liu, X., Millings, E.J., Okafor, C.D., Patel, A., Cato, M.L., Cornelison, J.C., Houtman, R., Moore, D.D., Calvert, J.W., Jui, N.T., Ortlund, E.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 30.35 kDa 
• Atom Count: 2,109 
• Modeled Residue Count: 250 
• Deposited Residue Count: 258 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 5 group A member 2	A	246	Homo sapiens	Mutation(s): 0  Gene Names: NR5A2, B1F, CPF, FTF
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens) Explore O00482  Go to UniProtKB:  O00482
PHAROS:  O00482 GTEx:  ENSG00000116833

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B [auth C]	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VQA (Subject of Investigation/LOI)	C [auth A]	10-[(3aR,6R,6aR)-6-hydroxy-3-phenyl-3a-(1-phenylethenyl)-1,3a,4,5,6,6a-hexahydropentalen-2-yl]decanoic acid C32 H40 O3 YGTFMMNUBBGVSN-LBRLCBGXSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VQA	BindingDB:  7JYD	EC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.37	α = 90
b = 88.37	β = 90
c = 105.674	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): D'Agostino, E.H., Mays, S.G., Ortlund, E.A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-1444932
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008602
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	F31DK111171
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008367-27
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK095750
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01DK114213
United States Department of Agriculture (USDA)	United States	3092-5-001-057

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description