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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24850 | |||||||||
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Title | Compressed conformation of nighttime state KaiC | |||||||||
![]() | Sharpened map | |||||||||
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![]() | AAA ATPase / Circadian Oscillator / Kinase / Phosphatase / CIRCADIAN CLOCK PROTEIN | |||||||||
Function / homology | ![]() 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 / 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / circadian rhythm / 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Sandate CR / Swan JA | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Coupling of distant ATPase domains in the circadian clock protein KaiC. Authors: Jeffrey A Swan / Colby R Sandate / Archana G Chavan / Alfred M Freeberg / Diana Etwaru / Dustin C Ernst / Joseph G Palacios / Susan S Golden / Andy LiWang / Gabriel C Lander / Carrie L Partch / ![]() Abstract: The AAA family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains ...The AAA family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains with tightly coupled activities, KaiC undergoes a cycle of autophosphorylation and autodephosphorylation on its C-terminal (CII) domain that restricts binding of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryogenic-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding on CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C-symmetric state at night, concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together, these studies clarify a key step in the regulation of cyanobacterial circadian rhythms by KaiC phosphorylation. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 25.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.7 KB 28.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.9 KB | Display | ![]() |
Images | ![]() | 84.5 KB | ||
Filedesc metadata | ![]() | 7.1 KB | ||
Others | ![]() ![]() ![]() | 19.8 MB 19.8 MB 19.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 916.2 KB | Display | ![]() |
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Full document | ![]() | 915.8 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s65MC ![]() 7s66C ![]() 7s67C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_24850_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_24850_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_24850_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Compressed state hexamer of nighttime state phosphomutant KaiC (K...
Entire | Name: Compressed state hexamer of nighttime state phosphomutant KaiC (KaiC-EA) |
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Components |
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-Supramolecule #1: Compressed state hexamer of nighttime state phosphomutant KaiC (K...
Supramolecule | Name: Compressed state hexamer of nighttime state phosphomutant KaiC (KaiC-EA) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 350 KDa |
-Macromolecule #1: Circadian clock protein kinase KaiC
Macromolecule | Name: Circadian clock protein kinase KaiC / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.084781 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTSAEMTSPN NNSEHQAIAK MRTMIEGFDD ISHGGLPIGR STLVSGTSGT GKTLFSIQFL YNGIIEFDEP GVFVTFEETP QDIIKNARS FGWDLAKLVD EGKLFILDAS PDPEGQEVVG GFDLSALIER INYAIQKYRA RRVSIDSVTS VFQQYDASSV V RRELFRLV ...String: MTSAEMTSPN NNSEHQAIAK MRTMIEGFDD ISHGGLPIGR STLVSGTSGT GKTLFSIQFL YNGIIEFDEP GVFVTFEETP QDIIKNARS FGWDLAKLVD EGKLFILDAS PDPEGQEVVG GFDLSALIER INYAIQKYRA RRVSIDSVTS VFQQYDASSV V RRELFRLV ARLKQIGATT VMTTERIEEY GPIARYGVEE FVSDNVVILR NVLEGERRRR TLEILKLRGT SHMKGEYPFT IT DHGINIF PLGAMRLTQR SSNVRVSSGV VRLDEMCGGG FFKDSIILAT GATGTGKTLL VSRFVENACA NKERAILFAY EES RAQLLR NAYSWGMDFE EMERQNLLKI VCAYPESAGL EDHLQIIKSE INDFKPARIA IDSLSALARG VSNNAFRQFV IGVT GYAKQ EEITGLFTNT SDQFMGAHSI TDSHIEAITD TIILLQYVEI RGEMSRAINV FKMRGSWHDK AIREFMISDK GPDIK DSFR NFERIISGSP TRITVDEKSE LSRIVRGVQE KGPES UniProtKB: Circadian clock oscillator protein KaiC |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 10 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation #1
Preparation ID | 1 | ||||||||||||||||||
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Concentration | 1.5 mg/mL | ||||||||||||||||||
Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER Details: Grids were plasma cleaned using Gatan Solarus (15 W for 7 s). | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER Details: Grids with applied sample were manually blotted with filter paper (Whatman No.1) for 3 seconds in a 4 C cold room before plunge freezing in liquid ethane cooled by liquid nitrogen.. |
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Sample preparation #2
Preparation ID | 2 | ||||||||||||||||||
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Concentration | 0.2 mg/mL | ||||||||||||||||||
Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER Details: Grids were plasma cleaned using Gatan Solarus (15 W for 7 s). | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER Details: Grids with applied sample were manually blotted with filter paper (Whatman No.1) for 3 seconds in a 4 C cold room before plunge freezing in liquid ethane cooled by liquid nitrogen.. | ||||||||||||||||||
Details | Sample was applied to holey C-flat grids, which previously had thin carbon floated on them. Grids were also pretreated with 0.1 % (w/v) poly-L-lysine hydrobromine (Polysciences). |
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Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TALOS ARCTICA |
Temperature | Min: 70.0 K / Max: 70.0 K |
Details | Sample was imaged at a 40 degree tilt. |
Image recording | Image recording ID: 1 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1137 / Average exposure time: 8.0 sec. / Average electron dose: 48.0 e/Å2 / Details: Tilted dataset |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: -1.7 µm / Calibrated defocus min: -0.8 µm / Calibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.7 µm / Nominal defocus min: -0.8 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TALOS ARCTICA |
Temperature | Min: 70.0 K / Max: 70.0 K |
Details | Sample was imaged at 0 degree tilt. |
Image recording | Image recording ID: 2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8405 / Average exposure time: 9.0 sec. / Average electron dose: 51.0 e/Å2 / Details: Thin carbon dataset |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |