5SY7 | pdb_00005sy7

Crystal Structure of the Heterodimeric NPAS3-ARNT Complex with HRE DNA

• PDB DOI: https://doi.org/10.2210/pdb5SY7/pdb
• NAKB: 5SY7

• Classification: transcription/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-10 Released: 2016-11-09 
• Deposition Author(s): Wu, D., Su, X., Potluri, N., Kim, Y., Rastinejad, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.361 (Depositor), 0.363 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: experimental

Literature

NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors.

Wu, D., Su, X., Potluri, N., Kim, Y., Rastinejad, F.

(2016) Elife 5

• PubMed: 27782878 
• DOI: https://doi.org/10.7554/eLife.18790
• Primary Citation Related Structures: 
  5SY5, 5SY7


• PubMed Abstract: 
  

  The neuronal PAS domain proteins NPAS1 and NPAS3 are members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family, and their genetic deficiencies are linked to a variety of human psychiatric disorders including schizophrenia, autism spectrum disorders and bipolar disease. NPAS1 and NPAS3 must each heterodimerize with the aryl hydrocarbon receptor nuclear translocator (ARNT), to form functional transcription complexes capable of DNA binding and gene regulation. Here we examined the crystal structures of multi-domain NPAS1-ARNT and NPAS3-ARNT-DNA complexes, discovering each to contain four putative ligand-binding pockets. Through expanded architectural comparisons between these complexes and HIF-1α-ARNT, HIF-2α-ARNT and CLOCK-BMAL1, we show the wider mammalian bHLH-PAS family is capable of multi-ligand-binding and presents as an ideal class of transcription factors for direct targeting by small-molecule drugs.

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Organizational Affiliation: 
• Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, United States.
Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, United States.

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: 102.55 kDa 
• Atom Count: 5,313 
• Modeled Residue Count: 594 
• Deposited Residue Count: 836 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	A	384	Mus musculus	Mutation(s): 0  Gene Names: Arnt
UniProt & NIH Common Fund Data Resources
Find proteins for P53762 (Mus musculus) Explore P53762  Go to UniProtKB:  P53762
IMPC:  MGI:88071

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal PAS domain-containing protein 3	B	410	Mus musculus	Mutation(s): 0  Gene Names: Npas3, Mop6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZQ0 (Mus musculus) Explore Q9QZQ0  Go to UniProtKB:  Q9QZQ0
IMPC:  MGI:1351610

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*TP*GP*CP*GP*TP*AP*CP*GP*TP*GP*CP*GP*GP*GP*TP*CP*GP*T)-3')	C	21	Mus musculus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*GP*AP*CP*CP*CP*GP*CP*AP*CP*GP*TP*AP*CP*GP*CP*AP*GP*C)-3')	D	21	Mus musculus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.361 (Depositor), 0.363 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.831	α = 90
b = 64.831	β = 90
c = 249.102	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Wu, D., Su, X., Potluri, N., Kim, Y., Rastinejad, F.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description