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- PDB-6qpj: Human CLOCK PAS-A domain -

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Basic information

Entry
Database: PDB / ID: 6qpj
TitleHuman CLOCK PAS-A domain
ComponentsCircadian locomoter output cycles protein kaput
KeywordsCIRCADIAN CLOCK PROTEIN / Circadian / CLOCK / PAS
Function / homology
Function and homology information


photoperiodism / CLOCK-BMAL transcription complex / regulation of hair cycle / negative regulation of glucocorticoid receptor signaling pathway / regulation of type B pancreatic cell development / chromatoid body / positive regulation of circadian rhythm / response to redox state / protein acetylation / E-box binding ...photoperiodism / CLOCK-BMAL transcription complex / regulation of hair cycle / negative regulation of glucocorticoid receptor signaling pathway / regulation of type B pancreatic cell development / chromatoid body / positive regulation of circadian rhythm / response to redox state / protein acetylation / E-box binding / regulation of insulin secretion / histone acetyltransferase activity / histone acetyltransferase / BMAL1:CLOCK,NPAS2 activates circadian gene expression / DNA damage checkpoint signaling / cellular response to ionizing radiation / circadian regulation of gene expression / Heme signaling / regulation of circadian rhythm / PPARA activates gene expression / chromatin DNA binding / positive regulation of inflammatory response / circadian rhythm / sequence-specific double-stranded DNA binding / Circadian Clock / chromosome / positive regulation of NF-kappaB transcription factor activity / HATs acetylate histones / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor 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 / DNA binding / nucleoplasm / nucleus / cytosol
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 / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...: / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Circadian locomoter output cycles protein kaput
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.315 Å
AuthorsKwon, H. / Freeman, S.L. / Moody, P.C.E. / Raven, E.L. / Basran, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006626/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Heme binding to human CLOCK affects interactions with the E-box.
Authors: Freeman, S.L. / Kwon, H. / Portolano, N. / Parkin, G. / Venkatraman Girija, U. / Basran, J. / Fielding, A.J. / Fairall, L. / Svistunenko, D.A. / Moody, P.C.E. / Schwabe, J.W.R. / Kyriacou, C.P. / Raven, E.L.
History
DepositionFeb 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)18,3151
Polymers18,3151
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.990, 45.360, 75.675
Angle α, β, γ (deg.)90.00, 93.46, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

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Components

#1: Protein Circadian locomoter output cycles protein kaput / hCLOCK / Class E basic helix-loop-helix protein 8 / bHLHe8


Mass: 18314.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLOCK, BHLHE8, KIAA0334 / Production host: Escherichia coli (E. coli) / References: UniProt: O15516, histone acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20 mM MES pH 6.5 0.1M Magnesium sulfate 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 6784 / % possible obs: 98.4 % / Redundancy: 3.4 % / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.4 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.315→25.063 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 296 4.36 %
Rwork0.1796 --
obs0.1826 6783 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.315→25.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 0 72 1133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091083
X-RAY DIFFRACTIONf_angle_d1.0011466
X-RAY DIFFRACTIONf_dihedral_angle_d3.345653
X-RAY DIFFRACTIONf_chiral_restr0.054170
X-RAY DIFFRACTIONf_plane_restr0.006186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.315-2.9160.3241400.17313154X-RAY DIFFRACTION97
2.916-25.06440.21291560.18223333X-RAY DIFFRACTION100

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