8HBM

Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA

• PDB DOI: https://doi.org/10.2210/pdb8HBM/pdb
• NAKB: 8HBM

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-29 Released: 2023-06-14 
• Deposition Author(s): Jiang, L., Chen, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.301 
• R-Value Work: 0.248 
• R-Value Observed: 0.253 

Literature

Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA

Jiang, L., Liu, X., Liang, X., Dai, S., Wei, H., Guo, M., Chen, Z., Xiao, D., Chen, Y.

(2023) Comput Struct Biotechnol J 21: 3149-3157

• DOI: https://doi.org/10.1016/j.csbj.2023.05.026

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.87 kDa 
• Atom Count: 3,633 
• Modelled Residue Count: 373 
• Deposited Residue Count: 472 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinoic acid receptor RXR-alpha	A, E	91	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
Bile acid receptor	B, F	109	Homo sapiens	Mutation(s): 0  Gene Names: NR1H4, BAR, FXR, HRR1, RIP14
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI1 (Homo sapiens) Explore Q96RI1  Go to UniProtKB:  Q96RI1
PHAROS:  Q96RI1 GTEx:  ENSG00000012504

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*AP*TP*GP*AP*CP*CP*TP*CP*G)-3')	C, G	18	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*AP*GP*GP*TP*CP*AP*TP*TP*GP*AP*CP*CP*TP*CP*G)-3')	D, H	18	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	I [auth A], J [auth A], K [auth B], L [auth B], M [auth E], N [auth E], O [auth F], P [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.301 
• R-Value Work: 0.248 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.65	α = 90
b = 60.016	β = 90
c = 241.797	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Jiang, L., Chen, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81974074 and 82172654

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description