6LB5

Crystal structure of dimeric RXR-LBD complexed with full agonist NEt-3IB and TIF2 co-activator

• PDB DOI: https://doi.org/10.2210/pdb6LB5/pdb

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


• Deposited: 2019-11-13 Released: 2020-11-18 
• Deposition Author(s): Imai, D., Numoto, N., Nakano, S., Kakuta, H., Ito, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Structural basis for the full and partial agonist activities of retinoid X receptor alpha ligands with an iso-butoxy and an isopropyl group

Imai, D., Numoto, N., Tokiwa, H., Kakuta, H., Ito, N.

(2024) Biochem Biophys Res Commun 734: 150617

• DOI: https://doi.org/10.1016/j.bbrc.2024.150617

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 58.12 kDa 
• Atom Count: 3,826 
• Modelled Residue Count: 452 
• Deposited Residue Count: 512 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A, C	243	Homo sapiens	Mutation(s): 0  Gene Names: RXRA, NR2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P19793 (Homo sapiens) Explore P19793  Go to UniProtKB:  P19793
PHAROS:  P19793 GTEx:  ENSG00000186350

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B, D	13	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
E80 (Subject of Investigation/LOI)	E [auth A], F [auth C]	6-[ethyl-[3-(2-methylpropoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid C21 H28 N2 O3 JUCWZKDTWSKUAW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E80	BindingDB:  6LB5	Ki: 182 (nM) from 1 assay(s)
		Kd: min: 340, max: 1300 (nM) from 2 assay(s)
		EC50: 19 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.240 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.411	α = 90
b = 64.026	β = 92.771
c = 46.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Imai, D., Numoto, N., Nakano, S., Kakuta, H., Ito, N.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2020-11-25
  Changes: Derived calculations
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-02
  Changes: Database references