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- PDB-5vji: Crystal structure of the CLOCK Transcription Domain Exon19 in Com... -

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Basic information

Entry
Database: PDB / ID: 5vji
TitleCrystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor
Components
  • CLOCK-interacting pacemaker
  • Circadian locomoter output cycles protein kaput
KeywordsTRANSCRIPTION / circadian rhythm / CLOCK protein / transcription activation / repressor / coiled coil / CIPC / circadian clock
Function / homology
Function and homology information


CLOCK-BMAL transcription complex / regulation of hair cycle / negative regulation of glucocorticoid receptor signaling pathway / regulation of type B pancreatic cell development / negative regulation of circadian rhythm / perichromatin fibrils / chromatoid body / positive regulation of circadian rhythm / response to redox state / protein acetylation ...CLOCK-BMAL transcription complex / regulation of hair cycle / negative regulation of glucocorticoid receptor signaling pathway / regulation of type B pancreatic cell development / negative regulation of circadian rhythm / perichromatin fibrils / chromatoid body / positive regulation of circadian rhythm / response to redox state / protein acetylation / E-box binding / histone acetyltransferase activity / histone acetyltransferase / regulation of insulin secretion / DNA damage checkpoint signaling / cellular response to ionizing radiation / circadian regulation of gene expression / regulation of circadian rhythm / chromatin DNA binding / positive regulation of inflammatory response / circadian rhythm / rhythmic process / positive regulation of NF-kappaB transcription factor activity / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription regulator complex / sequence-specific DNA binding / 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 / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Clock-interacting pacemaker / Clock interacting protein circadian / : / 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 domain / Myc-type, basic helix-loop-helix (bHLH) domain ...Clock-interacting pacemaker / Clock interacting protein circadian / : / 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 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
Similarity search - Domain/homology
Circadian locomoter output cycles protein kaput / CLOCK-interacting pacemaker
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsHou, Z. / Su, L. / Pei, J. / Grishin, N.V. / Zhang, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104496 United States
Welch FoundationI1505 United States
CitationJournal: Structure / Year: 2017
Title: Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor.
Authors: Hou, Z. / Su, L. / Pei, J. / Grishin, N.V. / Zhang, H.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Circadian locomoter output cycles protein kaput
B: Circadian locomoter output cycles protein kaput
C: CLOCK-interacting pacemaker
D: Circadian locomoter output cycles protein kaput
E: Circadian locomoter output cycles protein kaput
F: CLOCK-interacting pacemaker


Theoretical massNumber of molelcules
Total (without water)39,1966
Polymers39,1966
Non-polymers00
Water2,126118
1
A: Circadian locomoter output cycles protein kaput
B: Circadian locomoter output cycles protein kaput
C: CLOCK-interacting pacemaker


Theoretical massNumber of molelcules
Total (without water)19,5983
Polymers19,5983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-38 kcal/mol
Surface area9870 Å2
MethodPISA
2
D: Circadian locomoter output cycles protein kaput
E: Circadian locomoter output cycles protein kaput
F: CLOCK-interacting pacemaker


Theoretical massNumber of molelcules
Total (without water)19,5983
Polymers19,5983
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-39 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.339, 77.585, 150.363
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
Circadian locomoter output cycles protein kaput / mCLOCK


Mass: 6196.404 Da / Num. of mol.: 4 / Fragment: UNP Residues 516-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clock / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08785, histone acetyltransferase
#2: Protein CLOCK-interacting pacemaker / CLOCK-interacting circadian protein


Mass: 7205.107 Da / Num. of mol.: 2 / Fragment: UNP residues 352-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cipc, Kiaa1737 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R0W1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.3 / Details: 100mM Bis-tris pH7.3 27% PEG2000MME 1% beat-DDM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 24841 / % possible obs: 97.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.6
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 4.9 % / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→28.04 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 29.82
RfactorNum. reflection% reflection
Rfree0.2802 2128 5.05 %
Rwork0.2139 --
obs0.2174 22684 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 0 118 2527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122461
X-RAY DIFFRACTIONf_angle_d1.1693289
X-RAY DIFFRACTIONf_dihedral_angle_d16.5421591
X-RAY DIFFRACTIONf_chiral_restr0.057377
X-RAY DIFFRACTIONf_plane_restr0.007432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90330.2767860.29721488X-RAY DIFFRACTION52
1.9033-1.95090.4149790.27141898X-RAY DIFFRACTION65
1.9509-2.00360.31861300.23762224X-RAY DIFFRACTION75
2.0036-2.06250.32261500.22912520X-RAY DIFFRACTION88
2.0625-2.12910.31811320.23422865X-RAY DIFFRACTION98
2.1291-2.20510.29611420.21872959X-RAY DIFFRACTION99
2.2051-2.29340.28411580.21452841X-RAY DIFFRACTION99
2.2934-2.39770.29981250.19972960X-RAY DIFFRACTION99
2.3977-2.52410.27821440.20422873X-RAY DIFFRACTION99
2.5241-2.68210.26711390.21242941X-RAY DIFFRACTION99
2.6821-2.8890.28641430.22732887X-RAY DIFFRACTION99
2.889-3.17930.27691720.21292887X-RAY DIFFRACTION99
3.1793-3.63860.23831960.19582872X-RAY DIFFRACTION100
3.6386-4.5810.25491740.17412912X-RAY DIFFRACTION100
4.581-28.04310.31691580.24812870X-RAY DIFFRACTION98
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)
11.6426-1.2077-2.03232.76213.4014.8788-0.04-0.0508-0.07640.058-0.10870.13010.0662-0.20390.16930.0027-0.0105-0.00270.0431-0.03040.182515.262926.842490.0955
21.1175-0.01461.22711.2442-0.25821.4286-0.0222-0.04840.1185-0.2412-0.0426-0.1305-0.03590.507-0.1205-0.024-0.01360.00830.1385-0.04690.15623.181329.275373.3161
30.46240.2131-0.0631.59391.94633.7174-0.01480.0058-0.0684-0.304-0.10170.0902-0.2273-0.27930.2243-0.0812-0.0433-0.06310.0628-0.06890.167313.402333.310677.9561
40.63460.3294-0.11340.86030.52540.6743-0.06470.01070.0068-0.28780.0611-0.0343-0.27580.2134-0.09450.3565-0.1036-0.0290.0659-0.02370.177821.483848.995978.3312
50.98560.38760.39591.73022.58474.1739-0.11370.23670.0930.35620.12320.0985-0.3566-0.06810.1160.5150.110.02560.11980.01440.206213.271549.413161.4016
60.9945-0.574-1.32820.92851.63893.4122-0.1168-0.08980.04910.1059-0.07570.1227-0.0603-0.32890.20540.1930.0164-0.00380.1241-0.03590.149412.713543.843675.2434
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:50)
2X-RAY DIFFRACTION2(chain B and resseq 7:48)
3X-RAY DIFFRACTION3(chain C and resseq 2:63)
4X-RAY DIFFRACTION4(chain D and resseq 8:49)
5X-RAY DIFFRACTION5(chain E and resseq 1:49)
6X-RAY DIFFRACTION6(chain F and resseq 2:63)

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