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- PDB-1sv1: NMR structure of the ThKaiA180C-CIIABD complex (25-structure ensemble) -

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Basic information

Entry
Database: PDB / ID: 1sv1
TitleNMR structure of the ThKaiA180C-CIIABD complex (25-structure ensemble)
Components
  • Circadian clock protein KaiA
  • Circadian clock protein KaiC
KeywordsCIRCADIAN CLOCK PROTEIN / X-class Four Helix Bundle / Protein-peptide complex
Function / homology
Function and homology information


protein serine/threonine/tyrosine kinase activity / circadian rhythm / regulation of circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription ...protein serine/threonine/tyrosine kinase activity / circadian rhythm / regulation of circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding
Similarity search - Function
KaiA/RbsU domain / Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / KaiA/RbsU helical domain superfamily ...KaiA/RbsU domain / Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / KaiA/RbsU helical domain superfamily / Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / KaiC-like domain / KaiC / CheY-like superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Circadian clock oscillator protein KaiC / Circadian clock oscillator protein KaiA / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / Distance geometry, Simulated annealing
AuthorsVakonakis, I. / LiWang, A.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation.
Authors: Vakonakis, I. / LiWang, A.C.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 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 / 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

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Assembly

Deposited unit
A: Circadian clock protein KaiA
B: Circadian clock protein KaiA
C: Circadian clock protein KaiC
D: Circadian clock protein KaiC


Theoretical massNumber of molelcules
Total (without water)32,4494
Polymers32,4494
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50lowest energy structures that satisfy all experimental restraints
RepresentativeModel #11lowest energy

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Components

#1: Protein Circadian clock protein KaiA / ThKaiA180C


Mass: 12601.585 Da / Num. of mol.: 2 / Fragment: C-terminal residues 180-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: KaiA / Plasmid: pET32a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q79V62
#2: Protein/peptide Circadian clock protein KaiC / CIIABD


Mass: 3623.117 Da / Num. of mol.: 2 / Fragment: C-terminal residues 488-518
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: KaiC / Plasmid: pET32a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RR33, UniProt: Q79V60*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1224D 13C-separated NOESY
13213C-edited/12C-filtered 3D NOESY
1433D 13C-separated NOESY
15413C-edited/12C-filtered 3D NOESY
NMR detailsText: Assignments of ThKaiA180C and CIIABD were performed through CBCA(CO)NH, CBCANH, HBHA(CO)NH and HC(C)H-COSY experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM ThKaiA180C U-15N, 1.1 mM CIIABD, 20 mM NaCl, 20 mM Na2HPO4 pH 7.07 at 296K95% H2O/5% D2O
21.1 mM ThKaiA180C U-15N,13C, 1.1 mM CIIABD, 20 mM NaCl, 20 mM Na2HPO4 pH 7.07 at 296K100% D2O
31.2 mM ThKaiA180C, 1.2 mM CIIABD U-15N,13C, 20 mM NaCl, 20 mM Na2HPO4 pH 7.07 at 296K100% D2O
40.8 mM ThKaiA180C U-15N,13C, 0.8 mM ThKaiA180C, 1.6 mM CIIABD U-15N,13C, 20 mM NaCl, 20 mM Na2HPO4 pH 7.07 at 296K100% D2O
Sample conditionsIonic strength: 20 mM NaCl, 20 mM NaPi / pH: 7 / Pressure: ambient / Temperature: 323 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionClassification
VNMR6.1 Rev. Ccollection
NMRPipe2.1 Rev. 2002.044.17.08processing
PIPP4.2.6data analysis
XPLOR-NIH2.9.1structure solution
XPLOR-NIH2.9.1refinement
RefinementMethod: Distance geometry, Simulated annealing / Software ordinal: 1
Details: The structure is based on 2420 total restraints: 1858 are NOE derived, 58 are from hydrogen bonds, 244 are dihedral angles and 260 are 13C chemical shifts.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy structures that satisfy all experimental restraints
Conformers calculated total number: 50 / Conformers submitted total number: 25

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