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- PDB-4h10: Intermolecular recognition revealed by the complex structure of h... -

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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 / homology
Function and homology information


photoperiodism / CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / 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 ...photoperiodism / CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / 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 / chromatoid body / chromatin => GO:0000785 / 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 / aryl hydrocarbon receptor binding / regulation of insulin secretion / regulation of neurogenesis / histone acetyltransferase activity / histone acetyltransferase / BMAL1:CLOCK,NPAS2 activates circadian gene expression / DNA damage checkpoint signaling / cellular response to ionizing radiation / Hsp90 protein binding / circadian regulation of gene expression / Heme signaling / regulation of circadian rhythm / PPARA activates gene expression / PML body / chromatin DNA binding / positive regulation of inflammatory response / protein import into nucleus / circadian rhythm / positive regulation of canonical Wnt signaling pathway / Circadian Clock / sequence-specific double-stranded DNA binding / chromosome / positive regulation of NF-kappaB transcription factor activity / HATs acetylate histones / 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 / transcription cis-regulatory region binding / protein dimerization activity / 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 / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
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 / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain ...: / 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 / 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. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Aryl hydrocarbon receptor nuclear translocator-like protein 1 / Circadian locomoter output cycles protein kaput
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
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.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 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
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
Polymers26,4094
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-50 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
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-MP3121

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Components

#1: 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- ...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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARNTL, BHLHE5, BMAL1, MOP3, PASD3 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O00327
#2: Protein 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLOCK, BHLHE8, KIAA0334 / Plasmid: 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 / Source method: obtained synthetically / Details: synthesized single-strand DNA
#4: DNA chain E-box DNA antisense strand


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→38.8 Å / Num. all: 14060 / Num. obs: 14045 / % possible obs: 99.9 % / Redundancy: 19.8 % / Rsym value: 0.094 / Net I/σ(I): 33.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.402→38.8 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.244 704 5.01 %5%, randomly selected
Rwork0.1952 ---
obs0.1975 14045 99.57 %-
all-14060 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.974 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.6354 Å20 Å20 Å2
2---4.6354 Å2-0 Å2
3---9.2707 Å2
Refinement stepCycle: LAST / Resolution: 2.402→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 609 0 106 1673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071648
X-RAY DIFFRACTIONf_angle_d1.2552338
X-RAY DIFFRACTIONf_dihedral_angle_d25.07670
X-RAY DIFFRACTIONf_chiral_restr0.062266
X-RAY DIFFRACTIONf_plane_restr0.004195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.402-2.58710.35641660.29132580X-RAY DIFFRACTION99
2.5871-2.84740.32151320.27642663X-RAY DIFFRACTION100
2.8474-3.25930.24441380.20782655X-RAY DIFFRACTION100
3.2593-4.10560.21271250.17022669X-RAY DIFFRACTION99
4.1056-38.83630.20951430.1632774X-RAY DIFFRACTION100
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)
11.4830.32450.38830.7957-0.03010.7905-0.3613-0.2052-0.24580.00420.0309-0.0831-0.1695-0.28990.10530.2933-0.0833-0.03160.2302-0.03080.04826.8482-17.12319.8084
20.75150.6397-0.2981.336-0.00350.21590.01650.30960.2115-0.3779-0.0255-0.1456-0.2218-0.43860.11640.4028-0.0576-0.06150.3959-0.04310.014822.931-12.13045.7056
31.89510.5934-0.43833.5237-0.38712.2158-0.5776-0.1334-0.2577-1.317-0.0257-1.11190.45190.28780.45590.5122-0.18720.21640.097-0.02660.365934.9013-23.3106-2.4323
40.1568-0.430.40614.706-0.87751.3441-0.4493-0.0764-0.1077-0.66910.0912-1.55360.10370.02990.25110.3456-0.21870.20190.21160.02090.464737.8154-20.6268-0.5949
Refinement 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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