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- PDB-8rw6: Human Brain and muscle ARNT-like 1 (BMAL1_HUMAN) PAS-B domain -

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Basic information

Entry
Database: PDB / ID: 8rw6
TitleHuman Brain and muscle ARNT-like 1 (BMAL1_HUMAN) PAS-B domain
ComponentsBasic helix-loop-helix ARNT-like protein 1
KeywordsTRANSCRIPTION / Transcription factor / Circadian rhythm / SNC
Function / homology
Function and homology information


CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / positive regulation of protein acetylation / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / regulation of type B pancreatic cell development / aryl hydrocarbon receptor complex / regulation of cellular senescence / chromatoid body / positive regulation of circadian rhythm ...CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / positive regulation of protein acetylation / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / regulation of type B pancreatic cell development / aryl hydrocarbon receptor complex / regulation of cellular senescence / chromatoid body / positive regulation of circadian rhythm / oxidative stress-induced premature senescence / negative regulation of TOR signaling / negative regulation of cold-induced thermogenesis / response to redox state / negative regulation of fat cell differentiation / E-box binding / aryl hydrocarbon receptor binding / regulation of neurogenesis / energy homeostasis / NPAS4 regulates expression of target genes / regulation of insulin secretion / BMAL1:CLOCK,NPAS2 activates circadian expression / transcription coregulator activity / Hsp90 protein binding / circadian regulation of gene expression / Heme signaling / PPARA activates gene expression / PML body / circadian rhythm / sequence-specific double-stranded DNA binding / positive regulation of canonical Wnt signaling pathway / : / DNA-binding transcription factor binding / spermatogenesis / sequence-specific DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of cell cycle / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily ...: / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Basic helix-loop-helix ARNT-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsPu, H. / Rastinejad, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210664/Z/18/Z United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Pharmacological targeting of BMAL1 modulates circadian and immune pathways.
Authors: Pu, H. / Bailey, L.C. / Bauer, L.G. / Voronkov, M. / Baxter, M. / Huber, K.V.M. / Khorasanizadeh, S. / Ray, D. / Rastinejad, F.
History
DepositionFeb 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Basic helix-loop-helix ARNT-like protein 1


Theoretical massNumber of molelcules
Total (without water)13,1901
Polymers13,1901
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.236, 37.348, 76.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Basic helix-loop-helix ARNT-like protein 1 / Aryl hydrocarbon receptor nuclear translocator-like protein 1 / Basic-helix-loop-helix-PAS protein ...Aryl hydrocarbon receptor nuclear translocator-like protein 1 / Basic-helix-loop-helix-PAS protein MOP3 / Brain and muscle ARNT-like 1 / Class E basic helix-loop-helix protein 5 / bHLHe5 / Member of PAS protein 3 / PAS domain-containing protein 3 / bHLH-PAS protein JAP3


Mass: 13189.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMAL1, ARNTL, BHLHE5, MOP3, PASD3 / Production host: Escherichia coli (E. coli) / References: UniProt: O00327
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.63 Å3/Da / Density % sol: 24.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG3350, 0.15 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.51→38.06 Å / Num. obs: 14123 / % possible obs: 97.96 % / Redundancy: 13.1 % / CC1/2: 0.997 / Net I/σ(I): 7.22
Reflection shellResolution: 1.51→1.564 Å / Num. unique obs: 1365 / CC1/2: 0.729

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→38.06 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 400 4.97 %
Rwork0.2021 --
obs0.2044 8050 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 0 33 908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006897
X-RAY DIFFRACTIONf_angle_d0.8171213
X-RAY DIFFRACTIONf_dihedral_angle_d19.086322
X-RAY DIFFRACTIONf_chiral_restr0.058132
X-RAY DIFFRACTIONf_plane_restr0.005152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-2.090.32861250.24472496X-RAY DIFFRACTION100
2.1-2.640.2551330.21772512X-RAY DIFFRACTION100
2.64-38.060.21861420.18112642X-RAY DIFFRACTION100

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