8RW6 | pdb_00008rw6

Human Brain and muscle ARNT-like 1 (BMAL1_HUMAN) PAS-B domain

• PDB DOI: https://doi.org/10.2210/pdb8RW6/pdb

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


• Deposited: 2024-02-02 Released: 2025-02-05 
• Deposition Author(s): Pu, H., Rastinejad, F.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Pharmacological targeting of BMAL1 modulates circadian and immune pathways.

Pu, H., Bailey, L.C., Bauer, L.G., Voronkov, M., Baxter, M., Huber, K.V.M., Khorasanizadeh, S., Ray, D., Rastinejad, F.

(2025) Nat Chem Biol 21: 736-745

• PubMed: 40133642 
• DOI: https://doi.org/10.1038/s41589-025-01863-x
• Primary Citation Related Structures: 
  8RW6, 8RW8


• PubMed Abstract: 
  

  The basic helix-loop-helix PER-ARNT-SIM (bHLH-PAS) proteins BMAL1 and CLOCK heterodimerize to form the master transcription factor governing rhythmic gene expression. Owing to connections between circadian regulation and numerous physiological pathways, targeting the BMAL1-CLOCK complex pharmacologically is an attractive entry point for intervening in circadian-related processes. In this study, we developed a small molecule, Core Circadian Modulator (CCM), that targets the cavity in the PASB domain of BMAL1, causing it to expand, leading to conformational changes in the PASB domain and altering the functions of BMAL1 as a transcription factor. Biochemical, structural and cellular investigations validate the high level of selectivity of CCM in engaging BMAL1, enabling direct access to BMAL1-CLOCK cellular activities. CCM induces dose-dependent alterations in PER2-Luc oscillations and orchestrates the downregulation of inflammatory and phagocytic pathways in macrophages. These findings collectively reveal that the BMAL1 protein architecture is inherently configured to enable the binding of chemical ligands for functional modulation.

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Organizational Affiliation: 
• Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK.
Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, UK.
Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 13.19 kDa 
• Atom Count: 908 
• Modeled Residue Count: 106 
• Deposited Residue Count: 114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Basic helix-loop-helix ARNT-like protein 1	A [auth B]	114	Homo sapiens	Mutation(s): 0  Gene Names: BMAL1, ARNTL, BHLHE5, MOP3, PASD3
UniProt & NIH Common Fund Data Resources
Find proteins for O00327 (Homo sapiens) Explore O00327  Go to UniProtKB:  O00327
PHAROS:  O00327 GTEx:  ENSG00000133794

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.236	α = 90
b = 37.348	β = 90
c = 76.116	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-05 
Deposition Author(s): Pu, H., Rastinejad, F.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	210664/Z/18/Z

Revision History  

• Version 1.0: 2025-02-05
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Database references
• Version 1.2: 2025-05-07
  Changes: Database references