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- EMDB-70432: Extended conformation of dusk state KaiC -

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Basic information

Entry
Database: EMDB / ID: EMD-70432
TitleExtended conformation of dusk state KaiC
Map datasharpened map used for model building
Sample
  • Complex: KaiC hexamer
    • Protein or peptide: Circadian clock oscillator protein KaiC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAAA ATPase / circadian oscillator / kinase / phosphatase / CIRCADIAN CLOCK PROTEIN
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
Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsDzimianski JV / Crosby P / Balasco Serrao VH / Partch CL
Funding support United States, 2 items
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 JV / Crosby P / Balasco Serrao VH / Partch CL
History
DepositionApr 29, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70432.png

Downloads & links

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Map

FileDownload / File: emd_70432.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.32 Å/pix.
x 700 pix.
= 226.87 Å		0.32 Å/pix.
x 700 pix.
= 226.87 Å		0.32 Å/pix.
x 700 pix.
= 226.87 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.3241 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.8295333 - 1.1878642
Average (Standard dev.)0.00017050254 (±0.035853796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 226.87 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70432_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_70432_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_70432_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_70432_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KaiC hexamer

EntireName: KaiC hexamer
Components
  • Complex: KaiC hexamer
    • Protein or peptide: Circadian clock oscillator protein KaiC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: KaiC hexamer

SupramoleculeName: KaiC hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechococcus elongatus (bacteria)

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Macromolecule #1: Circadian clock oscillator protein KaiC

MacromoleculeName: Circadian clock oscillator protein KaiC / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 59.139801 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DYKDDDDKMT SAEMTSPNNN SEHQAIAKMR TMIEGFDDIS HGGLPIGRST LVSGTSGTGK TLFSIQFLYN GIIEFDEPGV FVTFEETPQ DIIKNARSFG WDLAKLVDEG KLFILDASPD PEGQEVVGGF DLSALIERIN YAIQKYRARR VSIDSVTSVF Q QYDASSVV ...String:
DYKDDDDKMT SAEMTSPNNN SEHQAIAKMR TMIEGFDDIS HGGLPIGRST LVSGTSGTGK TLFSIQFLYN GIIEFDEPGV FVTFEETPQ DIIKNARSFG WDLAKLVDEG KLFILDASPD PEGQEVVGGF DLSALIERIN YAIQKYRARR VSIDSVTSVF Q QYDASSVV RRELFRLVAR LKQIGATTVM TTERIEEYGP IARYGVEEFV SDNVVILRNV LEGERRRRTL EILKLRGTSH MK GEYPFTI TDHGINIFPL GAMRLTQRSS NVRVSSGVVR LDEMCGGGFF KDSIILATGA TGTGKTLLVS RFVENACANK ERA ILFAYE ESRAQLLRNA YSWGMDFEEM ERQNLLKIVC AYPESAGLED HLQIIKSEIN DFKPARIAID SLSALARGVS NNAF RQFVI GVTGYAKQEE ITGLFTNTSD QFMGAHSITD SHIEEITDTI ILLQYVEIRG EMSRAINVFK MRGSWHDKAI REFMI SDKG PDIKDSFRNF ERIISGSPTR ITVDEKSELS RIVRGVQEKG PES

UniProtKB: Circadian clock oscillator protein KaiC

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 2 / Number real images: 15001 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5642652
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 501579
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8jon


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9ofh:
Extended conformation of dusk state KaiC

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