8F8M | pdb_00008f8m

LRH-1 bound to small molecule Tet and fragment of coactivator Tif2

• PDB DOI: https://doi.org/10.2210/pdb8F8M/pdb

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


• Deposited: 2022-11-22 Released: 2023-11-29 
• Deposition Author(s): Cato, M.L., Ortlund, E.A.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Isosteric improvements to liver receptor homolog-1 small molecule modulators

Cato, M.L., Abraham, S.M., Spurlin, R.M., Flynn, A.R., Colucci, J.K., D'Agostino, E.H., Johnson, A.M., 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)

Macromolecule Content 

• Total Structure Weight: 30.61 kDa 
• Atom Count: 2,107 
• Modeled Residue Count: 251 
• Deposited Residue Count: 260 
• 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	14	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
XKE (Subject of Investigation/LOI)	C [auth A]	(1~{R},3~{a}~{R},6~{a}~{R})-4-phenyl-3~{a}-(1-phenylethenyl)-5-[9-(1~{H}-1,2,3,4-tetrazol-5-yl)nonyl]-2,3,6,6~{a}-tetrahydro-1~{H}-pentalen-1-ol C32 H40 N4 O KWRMCWKEHBRILN-LBRLCBGXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.161	α = 90
b = 89.161	β = 90
c = 105.692	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Cato, M.L., Ortlund, E.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	F31-DK122745
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	R01-DK115213
American Heart Association	United States	20PRE35200311
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008367-29
National Science Foundation (NSF, United States)	United States	DGE-1444932

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release