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Yorodumi- EMDB-29506: Structure of dodecameric KaiC-RS-S413E/S414E complexed with KaiB-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29506 | |||||||||
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Title | Structure of dodecameric KaiC-RS-S413E/S414E complexed with KaiB-RS solved by cryo-EM | |||||||||
Map data | Composite map of two hexamer reconstructions aligned and combined by taking the maximum absolute value | |||||||||
Sample |
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Keywords | autokinase / CIRCADIAN CLOCK PROTEIN | |||||||||
Function / homology | Function and homology information rhythmic process / kinase activity / non-specific serine/threonine protein kinase / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Cereibacter sphaeroides (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Padua RAP / Grant T / Pitsawong W / Hoemberger MS / Otten R / Bradshaw N / Grigorieff N / Kern D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 Title: From primordial clocks to circadian oscillators. Authors: Warintra Pitsawong / Ricardo A P Pádua / Timothy Grant / Marc Hoemberger / Renee Otten / Niels Bradshaw / Nikolaus Grigorieff / Dorothee Kern / Abstract: Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary ...Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock. Subsequent additions of KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood, but little is known about more ancient systems that only possess KaiBC. However, there are reports that they might exhibit a basic, hourglass-like timekeeping mechanism. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29506.map.gz | 348.3 MB | EMDB map data format | |
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Header (meta data) | emd-29506-v30.xml emd-29506.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_29506.png | 72 KB | ||
Filedesc metadata | emd-29506.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29506 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29506 | HTTPS FTP |
-Validation report
Summary document | emd_29506_validation.pdf.gz | 653.2 KB | Display | EMDB validaton report |
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Full document | emd_29506_full_validation.pdf.gz | 652.8 KB | Display | |
Data in XML | emd_29506_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_29506_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29506 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29506 | HTTPS FTP |
-Related structure data
Related structure data | 8fwjMC 8db3C 8dbaC 8fwiC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29506.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of two hexamer reconstructions aligned and combined by taking the maximum absolute value | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Dodecamer of KaiC-RS-S413E/S414E bound with KaiC-RS
Entire | Name: Dodecamer of KaiC-RS-S413E/S414E bound with KaiC-RS |
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Components |
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-Supramolecule #1: Dodecamer of KaiC-RS-S413E/S414E bound with KaiC-RS
Supramolecule | Name: Dodecamer of KaiC-RS-S413E/S414E bound with KaiC-RS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Cereibacter sphaeroides (bacteria) |
Molecular weight | Theoretical: 875 KDa |
-Macromolecule #1: Circadian clock protein KaiC
Macromolecule | Name: Circadian clock protein KaiC / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Cereibacter sphaeroides (bacteria) |
Molecular weight | Theoretical: 62.666133 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GAMGIGKSPT GIQGFDELTL GGLPTGRPSL VCGSAGCGKT LFASTFLING VRDHGEPGVF VTFEERPEDI VNNVASLGFE LDKLIEEEK IAIEHIAVDP SEVAEIGDYD LEGLFLRLEL AIDTVGAKRV VLDTIESLFS AFSNPAILRA EIRRLFDWLK E RGLTTVIT ...String: GAMGIGKSPT GIQGFDELTL GGLPTGRPSL VCGSAGCGKT LFASTFLING VRDHGEPGVF VTFEERPEDI VNNVASLGFE LDKLIEEEK IAIEHIAVDP SEVAEIGDYD LEGLFLRLEL AIDTVGAKRV VLDTIESLFS AFSNPAILRA EIRRLFDWLK E RGLTTVIT AERGDGALTR QGLEEYVSDC VILLDHRVEN QISTRRLRIV KYRGTAHGTN EYPFLIDTDG FSVLPVSALG LL HQVHEER IASGVPDLDA MMAGGGFFRG SSILVSGVAG AGKSSLAAHF AAAACARGER AMYFSFEEAA DQAVRNMRSL GLD LGRWRD AGLLRFMATR PTFYSLEMHL AVILREVMRF EPSVVVLDPI SAFTESGDRL EVQSMLLRIV DFLKNRGITG IFTH LAHSQ NEATTDAGLE ELMDGWVLML NREVNGEFNR ELYLLKARGM AHSNQVREFL MSDRGISLLP PHLGEGGALT GTARK AEEA RLRRAEIERQ TELGRLQQQI EQRRRRARAQ IEALEAELQA EEIALKALVE SESAHERQRL ADADTLARSR GNERFA DLL MNKGE UniProtKB: non-specific serine/threonine protein kinase |
-Macromolecule #2: Circadian clock protein KaiB
Macromolecule | Name: Circadian clock protein KaiB / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Cereibacter sphaeroides (bacteria) |
Molecular weight | Theoretical: 10.317127 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GAMGRRLVLY VAGQTPKSLA AISNLRRICE ENLPGQYEVE VIDLKQNPRL AKEHSIVAIP TLVRELPVPI RKIIGDLSDK EQVLVNLKM DME UniProtKB: Circadian clock protein KaiB |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 24 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 48 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Grid | Model: C-flat-1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8fwj: |