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- EMDB-36461: Structure of a synthetic circadian clock protein KaiC mutant of c... -

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Basic information

Entry
Database: EMDB / ID: EMD-36461
TitleStructure of a synthetic circadian clock protein KaiC mutant of cyanobacteria Synechococcus elongatus PCC 7942
Map dataCryo-EM map of anKaiC
Sample
  • Complex: Synthetic KaiC protein.
    • Protein or peptide: Circadian clock oscillator protein KaiC
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordscircadian clock protein / Synthetic protein / KaiC / BIOSYNTHETIC 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 / 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
Circadian clock oscillator protein KaiC
Similarity search - Component
Biological speciesSynechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsJia X / Zhang Q / Li S / Guo J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2025
Title: Reconstruction of the ancient cyanobacterial proto-circadian clock system KaiABC.
Authors: Silin Li / Zengxuan Zhou / Yufeng Wan / Xudong Jia / Peiliang Wang / Yu Wang / Taisen Zuo / He Cheng / Xiaoting Fang / Shuqi Dong / Jun He / Yilin Yang / Yichen Xu / Shaoxuan Fu / Xujing ...Authors: Silin Li / Zengxuan Zhou / Yufeng Wan / Xudong Jia / Peiliang Wang / Yu Wang / Taisen Zuo / He Cheng / Xiaoting Fang / Shuqi Dong / Jun He / Yilin Yang / Yichen Xu / Shaoxuan Fu / Xujing Wang / Ximing Qin / Qiguang Xie / Xiaodong Xu / Yuwei Zhao / Dan Liang / Peng Zhang / Qinfen Zhang / Jinhu Guo /
Abstract: Earlier in its history, the Earth used to spin faster than it does today. How ancient organisms adapted to the short day/night cycles during that time remains unclear. In this study we reconstruct ...Earlier in its history, the Earth used to spin faster than it does today. How ancient organisms adapted to the short day/night cycles during that time remains unclear. In this study we reconstruct and analyse the ancient circadian clock system KaiABC (anKaiABC) of cyanobacteria that existed ~0.95 billion years ago, when the daily light/dark cycle was ~18 h-long. Compared to their contemporary counterparts, anKaiABC proteins had different structures and interactions. The kinase, phosphatase, and adenosine triphosphatase (ATPase) activities of anKaiC were lower, while the anKaiA and anKaiB proteins were less effective at regulating the KaiC/anKaiC phosphorylation status. We provide evidence indicating that the anKaiABC system does not endogenously oscillate, but it can be entrained by an 18 h-long light/dark cycle. A Synechococcus strain expressing ankaiABC genes exhibits better adaptation to 9-h light/9-h dark cycles (LD9:9) that mimic the ancient 18-h day/night cycles, whereas the kaiABC-expressing strain preferentially adapts to the LD12:12 contemporary conditions. These findings suggest that, despite its lack of self-sustaining circadian oscillation, the proto-circadian system may have mediated adaptation of ancient cyanobacteria to the 18 h-long light/dark cycles present 0.95 billion years ago.
History
DepositionJun 7, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36461.png

Downloads & links

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Map

FileDownload / File: emd_36461.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of anKaiC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.71 Å/pix.
x 300 pix.
= 213. Å		0.71 Å/pix.
x 300 pix.
= 213. Å		0.71 Å/pix.
x 300 pix.
= 213. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.1398401 - 4.673848
Average (Standard dev.)-0.000000000000548 (±0.12961799)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 213.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_36461_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_36461_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Synthetic KaiC protein.

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

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Supramolecule #1: Synthetic KaiC protein.

SupramoleculeName: Synthetic KaiC protein. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (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 (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria)
Molecular weightTheoretical: 58.58909 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MTSLAEHTSP NNESSHQRLS EVQKMPTMIE GFDDISHGGL PTGRSTLVSG TSGTGKTLFS IQFLYNGITE FDEPGIFVTF EESPQDIIK NARSFGWNLQ KLVDQGKLFI LDASPDPDGQ EVAGGFDLSA LIERINYAIQ KYKARRVSID SVTAVFQQYD A ASVVRREI ...String:
MTSLAEHTSP NNESSHQRLS EVQKMPTMIE GFDDISHGGL PTGRSTLVSG TSGTGKTLFS IQFLYNGITE FDEPGIFVTF EESPQDIIK NARSFGWNLQ KLVDQGKLFI LDASPDPDGQ EVAGGFDLSA LIERINYAIQ KYKARRVSID SVTAVFQQYD A ASVVRREI FRLVARLKQI GVTTVMTTER IDEYGPIARY GVEEFVSDNV VILRNVLEGE RRRRTVEILK LRGTTHMKGE YP FTINDHG INIFPLGAMR LTQRSSNVRV SSGVPRLDEM CGGGFFKDSI ILATGATGTG KTLLVSKFIE NACQNKERAI LFA YEESRA QLLRNASSWG IDFEEMERQG LLKIICAYPE SAGLEDHLQI IKSEIGDFKP SRIAIDSLSA LARGVSNNAF RQFV IGVTG YAKQEEITGF FTNTSDQFMG SHSITDSHIS TITDTILLLQ YVEIRGEMSR AINVFKMRGS WHDKGIREYV ITDKG PEIK DSFRNFERII SGSPTRITVD EKSENLSRIA RGVQEKEPES

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: 6 / 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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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62981
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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