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- PDB-9ofh: Extended conformation of dusk state KaiC -

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Basic information

Entry
Database: PDB / ID: 9ofh
TitleExtended conformation of dusk state KaiC
ComponentsCircadian clock oscillator protein KaiC
KeywordsCIRCADIAN CLOCK PROTEIN / AAA ATPase / circadian oscillator / kinase / phosphatase
Function / homology
Function and homology information


regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription ...regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / circadian rhythm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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
Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsDzimianski, J.V. / Crosby, P. / Balasco Serrao, V.H. / Partch, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141849 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Extended conformation of dusk state KaiC
Authors: Dzimianski, J.V. / Crosby, P. / Balasco Serrao, V.H. / Partch, C.L.
History
DepositionApr 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Circadian clock oscillator protein KaiC
B: Circadian clock oscillator protein KaiC
C: Circadian clock oscillator protein KaiC
D: Circadian clock oscillator protein KaiC
E: Circadian clock oscillator protein KaiC
F: Circadian clock oscillator protein KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,21730
Polymers354,8396
Non-polymers6,37824
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "C"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAILEILEFF17 - 49725 - 505
d_12ATPATPATPATPFAA1001
d_13ATPATPATPATPFBA1002
d_14MGMGMGMGFCA1003
d_21ALAALAILEILEBB17 - 49725 - 505
d_22ATPATPATPATPBK1001
d_23ATPATPATPATPBL1002
d_24MGMGMGMGBM1003
d_31ALAALAILEILEAA17 - 49725 - 505
d_32ATPATPATPATPAG1001
d_33ATPATPATPATPAH1002
d_34MGMGMGMGAI1003
d_41ALAALAILEILEDD17 - 49725 - 505
d_42ATPATPATPATPDS1001
d_43ATPATPATPATPDT1002
d_44MGMGMGMGDU1003
d_51ALAALAILEILEEE17 - 49725 - 505
d_52ATPATPATPATPEW1001
d_53ATPATPATPATPEX1002
d_54MGMGMGMGEY1003
d_61ALAALAILEILECC17 - 49725 - 505
d_62ATPATPATPATPCO1001
d_63ATPATPATPATPCP1002
d_64MGMGMGMGCQ1003

NCS oper:
IDCodeMatrixVector
1given(-0.499993115233, -0.86602937794, -3.55671694044E-5), (0.866029377672, -0.499993112262, -6.85538575745E-5), (4.15863149057E-5, -6.50786703947E-5, 0.999999997018)268.380124995, 71.9576056731, 0.00265520306471
2given(0.50000196609, -0.866024268265, -2.61051077063E-5), (0.866024267639, 0.500001966737, -3.34447140819E-5), (4.20165392352E-5, -5.88523398673E-6, 0.9999999991)154.960042693, -41.4949996558, -0.00381508024671
3given(-0.500164379883, 0.865930445286, 0.00023879383083), (-0.865930476506, -0.500164377187, -7.5170589523E-5), (5.43436656151E-5, -0.000244376507012, 0.999999968663)71.8655304464, 268.411007762, 0.0240289535845
4given(0.499977566304, 0.866038354531, 4.09032479566E-5), (-0.866038354795, 0.499977567243, -1.66531215731E-5), (-3.48729484107E-5, -2.70975943706E-5, 0.999999999025)-41.5435893625, 154.94833685, 0.00699277587609
5given(-0.999999999848, 1.60743869088E-5, 6.77370332571E-6), (-1.60750022931E-5, -0.999999995743, -9.08587557575E-5), (6.77224279808E-6, -9.0858864631E-5, 0.999999995849)226.828122483, 226.911507518, 0.0094372674312

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Components

#1: Protein
Circadian clock oscillator protein KaiC


Mass: 59139.801 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: kaiC, Synpcc7942_1216, see0011 / Production host: Escherichia coli (E. coli)
References: UniProt: Q79PF4, non-specific serine/threonine protein kinase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: KaiC hexamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Synechococcus elongatus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 15001

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2SerialEM4.1image acquisition
4cryoSPARC4.2.1CTF correction
7UCSF ChimeraX1.8model fitting
9Coot0.9.8.95model refinement
10ISOLDE1.8model refinement
11PHENIX1.21.2_5419model refinement
12cryoSPARC4.4.1initial Euler assignment
13cryoSPARC4.4.1final Euler assignment
14cryoSPARC4.4.1classification
15cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5642652
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 501579 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8JON

8jon


Accession code: 8JON / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001422722
ELECTRON MICROSCOPYf_angle_d0.364130684
ELECTRON MICROSCOPYf_chiral_restr0.03963438
ELECTRON MICROSCOPYf_plane_restr0.00263894
ELECTRON MICROSCOPYf_dihedral_angle_d10.63838742
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FFELECTRON MICROSCOPYNCS constraints8.08054786058E-13
ens_1d_3FFELECTRON MICROSCOPYNCS constraints5.07144714819E-13
ens_1d_4FFELECTRON MICROSCOPYNCS constraints5.64063211343E-13
ens_1d_5FFELECTRON MICROSCOPYNCS constraints1.67940727639E-12
ens_1d_6FFELECTRON MICROSCOPYNCS constraints1.31854598203E-10

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