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- PDB-2kdk: Structure of human circadian clock protein BMAL2 C-terminal PAS domain -

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Basic information

Entry
Database: PDB / ID: 2kdk
TitleStructure of human circadian clock protein BMAL2 C-terminal PAS domain
ComponentsAryl hydrocarbon receptor nuclear translocator-like protein 2
KeywordsTRANSCRIPTION REGULATOR / circadian clock / PAS domain / transcription / Activator / Biological rhythms / DNA-binding / Nucleus / Transcription regulation
Function / homology
Function and homology information


CLOCK-BMAL transcription complex / aryl hydrocarbon receptor complex / entrainment of circadian clock / positive regulation of circadian rhythm / E-box binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / circadian regulation of gene expression / circadian rhythm / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific ...CLOCK-BMAL transcription complex / aryl hydrocarbon receptor complex / entrainment of circadian clock / positive regulation of circadian rhythm / E-box binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / circadian regulation of gene expression / circadian rhythm / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAS domain / PAS domain / Beta-Lactamase / 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 / PAS domain / PAS domain / Beta-Lactamase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Basic helix-loop-helix ARNT-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWasielewski, E. / Correia, C. / Prendergast, F.G. / Mer, G.
CitationJournal: To be Published
Title: Structure of human circadian clock protein BMAL2 C-terminal PAS domain
Authors: Correia, C. / Wasielewski, E. / Prendergast, F.G. / Mer, G.
History
DepositionJan 10, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Structure summary
Revision 1.3Oct 20, 2021Group: Data collection / Database references
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator-like protein 2


Theoretical massNumber of molelcules
Total (without water)13,8711
Polymers13,8711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Aryl hydrocarbon receptor nuclear translocator-like protein 2 / Brain and muscle ARNT-like 2 / Member of PAS protein 9 / Basic-helix-loop-helix-PAS protein MOP9 / ...Brain and muscle ARNT-like 2 / Member of PAS protein 9 / Basic-helix-loop-helix-PAS protein MOP9 / CYCLE-like factor / CLIF


Mass: 13870.537 Da / Num. of mol.: 1 / Mutation: W408D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNTL2, BMAL2, CLIF, MOP9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8WYA1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Circadian clock protein BMAL2 PAS-B domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1313D 1H-15N NOESY
1422D 1H-15N HSQC
1522D 1H-13C HSQC
1623D HNCO
1723D HN(CA)CB
1823D CBCA(CO)NH
1923D HBHA(CO)NH
11023D CCH-TOCSY
11123D CCH-COSY
11223D 1H-13C NOESY
11323D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 15N] BMAL2 PAS-B-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 2 mM DTT-4, 0.5 mM DSS-5, 93% H2O/7% D2O93% H2O/7% D2O
21.0 mM [U-100% 13C; U-100% 15N] BMAL2 PAS-B-6, 50 mM sodium phosphate-7, 50 mM sodium chloride-8, 2 mM DTT-9, 0.5 mM DSS-10, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMBMAL2 PAS-B-1[U-100% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
2 mMDTT-41
0.5 mMDSS-51
1.0 mMBMAL2 PAS-B-6[U-100% 13C; U-100% 15N]2
50 mMsodium phosphate-72
50 mMsodium chloride-82
2 mMDTT-92
0.5 mMDSS-102
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: AMBER 8.0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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