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- PDB-9ofg: CI ring of daytime state KaiC -

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Basic information

Entry
Database: PDB / ID: 9ofg
TitleCI ring of daytime state KaiC
ComponentsCircadian clock protein kinase 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity ...regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine 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: 3.35 Å
AuthorsDzimianski, J.V. / Sandate, C.R. / Balasco Serrao, V.H. / Lander, G.C. / Partch, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R21GM142196 United States
CitationJournal: To Be Published
Title: CI ring of daytime state KaiC
Authors: Dzimianski, J.V. / Sandate, C.R. / Balasco Serrao, V.H. / Lander, G.C. / 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: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Additional map / Part number: 3 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)351,69818
Polymers348,5096
Non-polymers3,18912
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 "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

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_11HISHISPROPROAA15 - 24815 - 248
d_12ATPATPATPATPAG1001
d_21HISHISPROPROBB15 - 24815 - 248
d_22ATPATPATPATPBI1001
d_31HISHISPROPROCC15 - 24815 - 248
d_32ATPATPATPATPCK1001
d_41HISHISPROPRODD15 - 24815 - 248
d_42ATPATPATPATPDM1001
d_51HISHISPROPROEE15 - 24815 - 248
d_52ATPATPATPATPEO1001
d_61HISHISPROPROFF15 - 24815 - 248
d_62ATPATPATPATPFQ1001

NCS oper:
IDCodeMatrixVector
1given(0.502274385679, 0.86470403996, 0.002713810604), (-0.864705398109, 0.502262098715, 0.00416637428496), (0.00223963646671, -0.00443930976321, 0.999987638202)-46.6871124778, 171.941158811, 0.237330519368
2given(-0.501798097119, 0.864984236676, -0.000969551593524), (-0.864978698269, -0.501798456983, -0.00318749291729), (-0.00324365062157, -0.000760836405205, 0.999994449914)80.5672280107, 299.753071746, 0.382529669866
3given(-0.999997479174, 0.00207967466521, 0.000846521087867), (-0.00208205286874, -0.999993861197, -0.00281826617702), (0.000840654814472, -0.00282002157432, 0.99999567038)252.670404613, 253.558353772, 0.227822721423
4given(-0.500933352894, -0.865485851688, -0.000128400510746), (0.865484574759, -0.500932347004, -0.00179849366113), (0.00149225084885, -0.00101205412127, 0.999998374466)299.331085412, 80.5610602625, 0.0123921672394
5given(0.500895674073, -0.865507374825, 0.000712614145473), (0.865499506665, 0.500894356562, 0.00393033417823), (-0.00375867762066, -0.00135192019619, 0.999992022295)172.617533168, -46.7718626569, 0.51068543732

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Components

#1: Protein
Circadian clock protein kinase KaiC


Mass: 58084.781 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
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / 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.: 6 / 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: Hexameric KaiC protein / 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
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2000 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 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1982
Image scansMovie frames/image: 85

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correction
7UCSF ChimeraX1.9model fitting
9ISOLDE1.9model refinement
10Coot0.9.8.95model refinement
11PHENIX1.21.2_5419model refinement
12cryoSPARC4.5.3initial Euler assignment
13cryoSPARC4.5.3final Euler assignment
14cryoSPARC4.5.3classification
15cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2641605
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 279379 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 7S66

7s66


Accession code: 7S66 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 42.51 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002811202
ELECTRON MICROSCOPYf_angle_d0.409115162
ELECTRON MICROSCOPYf_chiral_restr0.04061704
ELECTRON MICROSCOPYf_plane_restr0.00261926
ELECTRON MICROSCOPYf_dihedral_angle_d10.33314332
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints4.0691394902E-13
ens_1d_3AAELECTRON MICROSCOPYNCS constraints5.34616835349E-11
ens_1d_4AAELECTRON MICROSCOPYNCS constraints6.29037737717E-12
ens_1d_5AAELECTRON MICROSCOPYNCS constraints4.60505843368E-13
ens_1d_6AAELECTRON MICROSCOPYNCS constraints4.16505915712E-12

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