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Basic information

Entry
Database: PDB / ID: 4h10
TitleIntermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic Helix-Loop-Helix domains with E-box DNA
Components
  • Aryl hydrocarbon receptor nuclear translocator-like protein 1
  • Circadian locomoter output cycles protein kaput
  • E-box DNA antisense strand
  • E-box DNA sense strand
KeywordsTRANSCRIPTION/DNA / bHLH / circadian transcription / TRANSCRIPTION-DNA complex
Function / homologyPAS repeat profile. / PAC motif / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS domain / Nuclear translocator / PPARA activates gene expression / HATs acetylate histones / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Myc-type, basic helix-loop-helix (bHLH) domain / PAS fold ...PAS repeat profile. / PAC motif / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS domain / Nuclear translocator / PPARA activates gene expression / HATs acetylate histones / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Myc-type, basic helix-loop-helix (bHLH) domain / PAS fold / PAS domain superfamily / Helix-loop-helix DNA-binding domain superfamily / Helix-loop-helix DNA-binding domain / PAS fold / Circadian Clock / photoperiodism / regulation of hair cycle / positive regulation of skeletal muscle cell differentiation / negative regulation of glucocorticoid receptor signaling pathway / positive regulation of protein acetylation / maternal process involved in parturition / regulation of type B pancreatic cell development / regulation of cellular senescence / chromatoid body / bHLH transcription factor binding / positive regulation of circadian rhythm / negative regulation of TOR signaling / response to redox state / negative regulation of fat cell differentiation / oxidative stress-induced premature senescence / regulation of neurogenesis / negative regulation of cold-induced thermogenesis / E-box binding / protein acetylation / regulation of protein catabolic process / repressing transcription factor binding / regulation of insulin secretion / histone acetyltransferase / histone acetyltransferase activity / aryl hydrocarbon receptor binding / RNA polymerase II distal enhancer sequence-specific DNA binding / DNA damage checkpoint / regulation of cell cycle / Hsp90 protein binding / circadian regulation of gene expression / positive regulation of inflammatory response / chromatin DNA binding / cellular response to ionizing radiation / PML body / positive regulation of canonical Wnt signaling pathway / transcription regulatory region sequence-specific DNA binding / circadian rhythm / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome / spermatogenesis / transcription factor complex / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II proximal promoter sequence-specific DNA binding / positive regulation of NF-kappaB transcription factor activity / protein dimerization activity / sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of transcription, DNA-templated / regulation of transcription, DNA-templated / DNA-binding transcription factor activity / protein heterodimerization activity / positive regulation of transcription, DNA-templated / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / Aryl hydrocarbon receptor nuclear translocator-like protein 1 / Circadian locomoter output cycles protein kaput
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.402 Å resolution
AuthorsWang, Z. / Su, X.-D.
CitationJournal: Cell Res. / Year: 2013
Title: Intermolecular recognition revealed by the complex structure of human CLOCK-BMAL1 basic helix-loop-helix domains with E-box DNA.
Authors: Wang, Z. / Wu, Y. / Li, L. / Su, X.D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 10, 2012 / Release: Dec 26, 2012
RevisionDateData content typeGroupProviderType
1.0Dec 26, 2012Structure modelrepositoryInitial release
1.1Feb 20, 2013Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor nuclear translocator-like protein 1
B: Circadian locomoter output cycles protein kaput
C: E-box DNA sense strand
D: E-box DNA antisense strand


Theoretical massNumber of molelcules
Total (without water)26,4094
Polyers26,4094
Non-polymers00
Water1,910106
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)5890
ΔGint (kcal/M)-50
Surface area (Å2)12150
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)98.740, 98.740, 62.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

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Components

#1: Protein/peptide 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: 8693.161 Da / Num. of mol.: 1 / Fragment: UNP residues 66-128 / Source: (gene. exp.) Homo sapiens (human) / Gene: ARNTL, BHLHE5, BMAL1, MOP3, PASD3 / Plasmid name: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O00327
#2: Protein/peptide Circadian locomoter output cycles protein kaput / hCLOCK / Class E basic helix-loop-helix protein 8 / bHLHe8


Mass: 8535.914 Da / Num. of mol.: 1 / Fragment: UNP residues 29-89 / Source: (gene. exp.) Homo sapiens (human) / Gene: CLOCK, BHLHE8, KIAA0334 / Plasmid name: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O15516, histone acetyltransferase
#3: DNA chain E-box DNA sense strand


Mass: 4588.001 Da / Num. of mol.: 1 / Details: synthesized single-strand DNA
#4: DNA chain E-box DNA antisense strand


Mass: 4591.969 Da / Num. of mol.: 1 / Details: synthesized single-strand DNA
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Formula: H2O / Water

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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: 3.35 / Density percent sol: 63.29 %
Crystal growTemp: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 20% (w/v) PEG 3350 and 0.2 M magnesium formate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Feb 25, 2011
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.4 Å / D resolution low: 38.8 Å / Number all: 14060 / Number obs: 14045 / Rsym value: 0.094 / NetI over sigmaI: 33.5 / Redundancy: 19.8 % / Percent possible obs: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.35 / R Free selection details: 5%, randomly selected / Sigma F: 0 / Overall phase error: 25.14 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.61 Å / Solvent vdw probe radii: 0.9 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 49.974 / Solvent model param ksol: 0.336
Displacement parametersAniso B11: -4.6354 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -4.6354 Å2 / Aniso B23: - Å2 / Aniso B33: 9.2707 Å2
Least-squares processR factor R free: 0.244 / R factor R work: 0.1952 / R factor obs: 0.1975 / Highest resolution: 2.402 Å / Lowest resolution: 38.8 Å / Number reflection R free: 704 / Number reflection all: 14060 / Number reflection obs: 14045 / Percent reflection R free: 5.01 / Percent reflection obs: 99.57
Refine hist #LASTHighest resolution: 2.402 Å / Lowest resolution: 38.8 Å
Number of atoms included #LASTProtein: 958 / Nucleic acid: 609 / Ligand: 0 / Solvent: 106 / Total: 1673
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071648
X-RAY DIFFRACTIONf_angle_d1.2552338
X-RAY DIFFRACTIONf_dihedral_angle_d25.070670
X-RAY DIFFRACTIONf_chiral_restr0.062266
X-RAY DIFFRACTIONf_plane_restr0.004195
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.4020.35640.29132.5871166258099.00
2.58710.32150.27642.84741322663100.00
2.84740.24440.20783.25931382655100.00
3.25930.21270.17024.1056125266999.00
4.10560.20950.163038.83631432774100.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.48300.32450.38830.7957-0.03010.7905-0.3613-0.2052-0.24580.00420.0309-0.0831-0.1695-0.28990.10530.2933-0.0833-0.03160.2302-0.03080.048026.8482-17.12319.8084
20.75150.6397-0.29801.3360-0.00350.21590.01650.30960.2115-0.3779-0.0255-0.1456-0.2218-0.43860.11640.4028-0.0576-0.06150.3959-0.04310.014822.9310-12.13045.7056
31.89510.5934-0.43833.5237-0.38712.2158-0.5776-0.1334-0.2577-1.3170-0.0257-1.11190.45190.28780.45590.5122-0.18720.21640.0970-0.02660.365934.9013-23.3106-2.4323
40.1568-0.43000.40614.7060-0.87751.3441-0.4493-0.0764-0.1077-0.66910.0912-1.55360.10370.02990.25110.3456-0.21870.20190.21160.02090.464737.8154-20.6268-0.5949
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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