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- PDB-4f3l: Crystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptiona... -

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Basic information

Entry
Database: PDB / ID: 4f3l
TitleCrystal Structure of the Heterodimeric CLOCK:BMAL1 Transcriptional Activator Complex
Components
  • BMAL1b
  • Circadian locomoter output cycles protein kaput
KeywordsTRANSCRIPTION/ACTIVATOR / bHLH / PAS / Circadian rhythm proteins / TRANSCRIPTION-ACTIVATOR complex
Function / homology
Function and homology information


CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / NPAS4 regulates expression of target genes / positive regulation of protein acetylation / negative regulation of glucocorticoid receptor signaling pathway / maternal process involved in parturition / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence ...CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / NPAS4 regulates expression of target genes / positive regulation of protein acetylation / negative regulation of glucocorticoid receptor signaling pathway / maternal process involved in parturition / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence / aryl hydrocarbon receptor complex / perichromatin fibrils / chromatoid body / negative regulation of TOR signaling / positive regulation of circadian rhythm / oxidative stress-induced premature senescence / negative regulation of cold-induced thermogenesis / response to redox state / negative regulation of fat cell differentiation / protein acetylation / regulation of protein catabolic process / E-box binding / regulation of insulin secretion / aryl hydrocarbon receptor binding / regulation of neurogenesis / histone acetyltransferase activity / histone acetyltransferase / DNA damage checkpoint signaling / cellular response to ionizing radiation / Hsp90 protein binding / circadian regulation of gene expression / regulation of circadian rhythm / PML body / chromatin DNA binding / autophagy / positive regulation of inflammatory response / protein import into nucleus / circadian rhythm / positive regulation of canonical Wnt signaling pathway / sequence-specific double-stranded DNA binding / gene expression / chromosome / positive regulation of NF-kappaB transcription factor activity / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / protein dimerization activity / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / 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 / PAS domain / Helix-loop-helix DNA-binding domain superfamily ...: / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / 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 / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Circadian locomoter output cycles protein kaput / BMAL1b / Basic helix-loop-helix ARNT-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.268 Å
AuthorsHuang, N. / Chelliah, Y. / Shan, Y. / Taylor, C. / Yoo, S. / Partch, C. / Green, C.B. / Zhang, H. / Takahashi, J.
CitationJournal: Science / Year: 2012
Title: Crystal structure of the heterodimeric CLOCK:BMAL1 transcriptional activator complex.
Authors: Huang, N. / Chelliah, Y. / Shan, Y. / Taylor, C.A. / Yoo, S.H. / Partch, C. / Green, C.B. / Zhang, H. / Takahashi, J.S.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Dec 5, 2018Group: Data collection / Category: diffrn_radiation_wavelength
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: BMAL1b
A: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)86,2762
Polymers86,2762
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-73 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.242, 71.955, 173.306
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 BMAL1b


Mass: 44192.676 Da / Num. of mol.: 1 / Fragment: UNP residues 62-447
Source method: isolated from a genetically manipulated source
Details: pFASTBac1 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arntl, BMAL1, bmal1b / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6F6D6, UniProt: Q9WTL8*PLUS
#2: Protein Circadian locomoter output cycles protein kaput / mCLOCK


Mass: 42083.410 Da / Num. of mol.: 1 / Fragment: UNP residues 26-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clock / Plasmid: pFASTBacHT / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O08785, histone acetyltransferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 100 mM Hepes pH 8.0, 6% PEG 3350 and 75 mM NaF., VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
3771
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 19-ID1
SYNCHROTRONALS 8.2.12
SYNCHROTRONAPS 19-ID3
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 15, 2011
ADSC QUANTUM 315r2CCDMay 10, 2011
ADSC QUANTUM 3153CCDApr 15, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.268→50 Å / Num. obs: 39307 / % possible obs: 99.5 %

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.268→37.117 Å / SU ML: 0.28 / σ(F): 0.06 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 1849 5.03 %
Rwork0.1843 --
obs0.186 36738 92.26 %
all-39307 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.7601 Å2-0 Å20 Å2
2---3.545 Å2-0 Å2
3---10.3051 Å2
Refinement stepCycle: LAST / Resolution: 2.268→37.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5068 0 0 177 5245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055220
X-RAY DIFFRACTIONf_angle_d0.8897041
X-RAY DIFFRACTIONf_dihedral_angle_d12.0411943
X-RAY DIFFRACTIONf_chiral_restr0.064769
X-RAY DIFFRACTIONf_plane_restr0.003892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.268-2.32910.29381000.24212056X-RAY DIFFRACTION71
2.3291-2.39760.26641380.22492458X-RAY DIFFRACTION86
2.3976-2.4750.29131340.21692539X-RAY DIFFRACTION89
2.475-2.56350.27221310.20152595X-RAY DIFFRACTION91
2.5635-2.66610.22841370.22594X-RAY DIFFRACTION90
2.6661-2.78740.21051500.19492628X-RAY DIFFRACTION92
2.7874-2.93430.2591470.19272751X-RAY DIFFRACTION95
2.9343-3.1180.24441350.1922806X-RAY DIFFRACTION97
3.118-3.35860.21971550.1822826X-RAY DIFFRACTION98
3.3586-3.69630.17731410.16372854X-RAY DIFFRACTION97
3.6963-4.23060.19241490.15062895X-RAY DIFFRACTION98
4.2306-5.32750.15731650.1432916X-RAY DIFFRACTION99
5.3275-37.12210.23921670.20442971X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4761-0.1382-0.60021.22370.35151.27060.1195-0.87230.77380.2661-0.34910.71050.0343-0.55740.19540.4567-0.0710.02291.0982-0.20260.6882-18.9878-20.5324137.6171
22.9393-0.3116-0.32380.69950.80833.2245-0.0802-0.1461-0.61240.312-0.08340.3910.6164-0.20870.13470.3385-0.05890.07250.1734-0.0780.4045.4777-6.7005163.8574
31.8314-0.17610.35481.3575-0.48051.88960.0206-0.0042-0.27730.3895-0.17340.0074-0.15560.18560.13340.34870.0162-0.0520.2533-0.02060.333212.5864-3.9216166.0318
45.27173.9745-2.23093.502-3.12576.20540.24760.9136-1.53650.2012-0.414-1.3674-0.43741.1365-0.07410.40570.0997-0.06740.7431-0.33010.676734.6861-3.9592152.7657
59.00715.40322.00036.16397.57391.99960.6649-0.128-0.2359-0.3643-0.00780.17430.2670.8687-0.53430.378-0.1194-0.1130.347-0.04180.209929.09589.7434164.3853
60.2903-0.0552-0.05871.0394-0.07460.2850.2227-0.03470.4459-0.1022-0.3784-0.48230.1628-0.38670.10940.4384-0.0848-0.04940.8180.0120.4-10.1111-21.0796135.3357
70.2319-0.1180.1241.9960.91633.15110.05570.4922-0.3026-0.2443-0.31080.2044-0.2479-0.08780.23590.31870.1005-0.02360.5862-0.25820.404416.5606-7.9082141.4219
81.4852-0.08850.70012.3355-0.27711.6444-0.03620.4145-0.1349-0.32530.0439-0.15510.11980.1433-0.03930.39070.05720.02820.554-0.35060.57219.0232-12.1482140.8076
90.31130.00820.38760.28480.11490.3454-0.08550.11870.1390.1016-0.0323-0.1394-0.1417-0.02960.10840.43210.096-0.07360.4979-0.1120.450814.94076.3958150.3805
103.93940.8370.75572.3907-0.42521.5990.02160.30840.5115-0.2378-0.15980.0779-0.1910.0670.10130.26730.05280.01790.22690.04080.261617.259425.0398156.2887
11-0.19760.18620.1744-0.26270.0369-0.12950.010.14-0.0496-0.06020.0023-0.00010.01210.04540.00130.32710.0395-0.01810.3726-0.03930.325522.536711.5393161.6305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 71:139 )B71 - 139
2X-RAY DIFFRACTION2( CHAIN B AND RESID 140:239 )B140 - 239
3X-RAY DIFFRACTION3( CHAIN B AND RESID 240:326 )B240 - 326
4X-RAY DIFFRACTION4( CHAIN B AND RESID 327:340 )B327 - 340
5X-RAY DIFFRACTION5( CHAIN B AND RESID 341:342 )B341 - 342
6X-RAY DIFFRACTION6( CHAIN A AND RESID 42:97 )A42 - 97
7X-RAY DIFFRACTION7( CHAIN A AND RESID 98:177 )A98 - 177
8X-RAY DIFFRACTION8( CHAIN A AND RESID 178:255 )A178 - 255
9X-RAY DIFFRACTION9( CHAIN A AND RESID 256:275 )A256 - 275
10X-RAY DIFFRACTION10( CHAIN A AND RESID 276:384 )A276 - 384
11X-RAY DIFFRACTION11( CHAIN A AND RESID 401:488 ) OR ( CHAIN B AND RESID 501:589 )A401 - 488
12X-RAY DIFFRACTION11( CHAIN A AND RESID 401:488 ) OR ( CHAIN B AND RESID 501:589 )B501 - 589

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