6LB4

Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator

• PDB DOI: https://doi.org/10.2210/pdb6LB4/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: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Crystal structure of dimeric RXR-LBD complexed with NEt-3ME and TIF2 co-activator

Imai, D., Numoto, N., Nakano, S., Kakuta, H., Ito, N.

To be published.

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.31 kDa 
• Atom Count: 2,150 
• Modelled Residue Count: 228 
• Deposited Residue Count: 256 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A	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	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E8L (Subject of Investigation/LOI)	C [auth A]	6-[ethyl-[3-(2-methoxyethoxy)-4-propan-2-yl-phenyl]amino]pyridine-3-carboxylic acid C20 H26 N2 O4 VVNCNFPVMMKHFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.298	α = 90
b = 66.298	β = 90
c = 109.669	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