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

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Basic information

Entry
Database: PDB / ID: 5vjx
TitleCrystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor
Components
  • CLOCK-interacting pacemaker
  • Circadian locomoter output cycles protein kaput
KeywordsTRANSFERASE / 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 / regulation of insulin secretion / histone acetyltransferase activity / histone acetyltransferase / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / 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 / cytoplasm / cytosol
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 DNA-binding domain superfamily / helix loop helix 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 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
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 / Resolution: 2.695 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 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLOCK-interacting pacemaker
B: Circadian locomoter output cycles protein kaput
C: Circadian locomoter output cycles protein kaput
D: CLOCK-interacting pacemaker
E: Circadian locomoter output cycles protein kaput
F: Circadian locomoter output cycles protein kaput
G: CLOCK-interacting pacemaker
H: Circadian locomoter output cycles protein kaput
I: Circadian locomoter output cycles protein kaput
J: CLOCK-interacting pacemaker
K: Circadian locomoter output cycles protein kaput
L: Circadian locomoter output cycles protein kaput
M: CLOCK-interacting pacemaker
N: Circadian locomoter output cycles protein kaput
O: Circadian locomoter output cycles protein kaput
R: CLOCK-interacting pacemaker
S: Circadian locomoter output cycles protein kaput
T: Circadian locomoter output cycles protein kaput
U: CLOCK-interacting pacemaker
V: Circadian locomoter output cycles protein kaput
W: Circadian locomoter output cycles protein kaput
X: CLOCK-interacting pacemaker
Y: Circadian locomoter output cycles protein kaput
Z: Circadian locomoter output cycles protein kaput
a: CLOCK-interacting pacemaker
b: Circadian locomoter output cycles protein kaput
c: Circadian locomoter output cycles protein kaput
d: CLOCK-interacting pacemaker
e: Circadian locomoter output cycles protein kaput
f: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)195,97930
Polymers195,97930
Non-polymers00
Water6,089338
1
A: CLOCK-interacting pacemaker
B: Circadian locomoter output cycles protein kaput
C: Circadian locomoter output cycles protein kaput
a: CLOCK-interacting pacemaker
b: Circadian locomoter output cycles protein kaput
c: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)39,1966
Polymers39,1966
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-85 kcal/mol
Surface area15400 Å2
MethodPISA
2
D: CLOCK-interacting pacemaker
E: Circadian locomoter output cycles protein kaput
F: Circadian locomoter output cycles protein kaput
J: CLOCK-interacting pacemaker
K: Circadian locomoter output cycles protein kaput
L: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)39,1966
Polymers39,1966
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-92 kcal/mol
Surface area18020 Å2
MethodPISA
3
G: CLOCK-interacting pacemaker
H: Circadian locomoter output cycles protein kaput
I: Circadian locomoter output cycles protein kaput
U: CLOCK-interacting pacemaker
V: Circadian locomoter output cycles protein kaput
W: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)39,1966
Polymers39,1966
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-96 kcal/mol
Surface area18500 Å2
MethodPISA
4
M: CLOCK-interacting pacemaker
N: Circadian locomoter output cycles protein kaput
O: Circadian locomoter output cycles protein kaput

R: CLOCK-interacting pacemaker
S: Circadian locomoter output cycles protein kaput
T: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)39,1966
Polymers39,1966
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12760 Å2
ΔGint-86 kcal/mol
Surface area17580 Å2
MethodPISA
5
X: CLOCK-interacting pacemaker
Y: Circadian locomoter output cycles protein kaput
Z: Circadian locomoter output cycles protein kaput
d: CLOCK-interacting pacemaker
e: Circadian locomoter output cycles protein kaput
f: Circadian locomoter output cycles protein kaput


Theoretical massNumber of molelcules
Total (without water)39,1966
Polymers39,1966
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-82 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.536, 116.836, 132.926
Angle α, β, γ (deg.)90.00, 126.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11a-101-

HOH

21c-104-

HOH

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Components

#1: Protein
CLOCK-interacting pacemaker / CLOCK-interacting circadian protein


Mass: 7205.107 Da / Num. of mol.: 10 / 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) / References: UniProt: Q8R0W1
#2: Protein
Circadian locomoter output cycles protein kaput / mCLOCK


Mass: 6196.404 Da / Num. of mol.: 20 / 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) / References: UniProt: O08785, histone acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8
Details: 100mM Hepes pH 8.0, 200mM Proline, 15% PEG3350, 3% myo-Inositiol (w/v)

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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: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.695→50 Å / Num. obs: 59416 / % possible obs: 99.9 % / Redundancy: 5.7 % / Net I/σ(I): 16.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 2.695→47.307 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2749 2721 5.11 %
Rwork0.2179 --
obs0.2208 53213 89.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.695→47.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12210 0 0 338 12548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01412340
X-RAY DIFFRACTIONf_angle_d1.42916483
X-RAY DIFFRACTIONf_dihedral_angle_d15.9524972
X-RAY DIFFRACTIONf_chiral_restr0.0691862
X-RAY DIFFRACTIONf_plane_restr0.0072172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6949-2.74390.4536370.3041562X-RAY DIFFRACTION19
2.7439-2.79660.3095700.30731231X-RAY DIFFRACTION42
2.7966-2.85370.39651240.28321912X-RAY DIFFRACTION64
2.8537-2.91570.38361120.272373X-RAY DIFFRACTION80
2.9157-2.98360.3441450.26972790X-RAY DIFFRACTION94
2.9836-3.05820.3051450.26482942X-RAY DIFFRACTION99
3.0582-3.14080.33011570.27662958X-RAY DIFFRACTION100
3.1408-3.23320.34011600.26222958X-RAY DIFFRACTION100
3.2332-3.33760.28891700.24582963X-RAY DIFFRACTION100
3.3376-3.45680.3071810.23012930X-RAY DIFFRACTION100
3.4568-3.59520.29111680.21492975X-RAY DIFFRACTION100
3.5952-3.75870.25521310.22362942X-RAY DIFFRACTION98
3.7587-3.95680.25061670.18762955X-RAY DIFFRACTION100
3.9568-4.20460.26621760.19122986X-RAY DIFFRACTION100
4.2046-4.5290.22411560.1762975X-RAY DIFFRACTION100
4.529-4.98430.20881590.17462979X-RAY DIFFRACTION100
4.9843-5.70450.27851620.21822985X-RAY DIFFRACTION100
5.7045-7.1830.33031680.26163005X-RAY DIFFRACTION100
7.183-47.31460.19121330.17563071X-RAY DIFFRACTION99

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