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- EMDB-29508: Structure of dodecameric KaiC-RS-S413E/S414E with bound KaiB-RS -... -
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Open data
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Basic information
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Title | Structure of dodecameric KaiC-RS-S413E/S414E with bound KaiB-RS - single hexamer focus map | |||||||||
![]() | KaiC-RS-S413E/S414E with bound KaiB-RS sharpened map with refinement focused on a single hexamer | |||||||||
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![]() | autokinase / CIRCADIAN CLOCK PROTEIN | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Padua RAP / Grant T / Pitsawong W / Hoemberger MS / Otten R / Bradshaw N / Grigorieff N / Kern D | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 285.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.5 KB | Display | ![]() |
Images | ![]() | 93.8 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Others | ![]() ![]() | 284.7 MB 284.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | KaiC-RS-S413E/S414E with bound KaiB-RS sharpened map with refinement focused on a single hexamer | ||||||||||||||||||||
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
-Half map: unsharpened half map
File | emd_29508_half_map_1.map | ||||||||||||
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Annotation | unsharpened half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unsharpened half map
File | emd_29508_half_map_2.map | ||||||||||||
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Annotation | unsharpened half map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dodecamer of KaiC-RS-S413E/S414E
Entire | Name: Dodecamer of KaiC-RS-S413E/S414E |
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Components |
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-Supramolecule #1: Dodecamer of KaiC-RS-S413E/S414E
Supramolecule | Name: Dodecamer of KaiC-RS-S413E/S414E / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 751 KDa |
-Macromolecule #1: KaiC-RS-S413E/S414E
Macromolecule | Name: KaiC-RS-S413E/S414E / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAMGIGKSPT GIQGFDELTL GGLPTGRPSL VCGSAGCGKT LFASTFLING VRDHGEPGVF VTFEERPEDI VNNVASLGFE LDKLIEEEKI AIEHIAVDPS EVAEIGDYDL EGLFLRLELA IDTVGAKRVV LDTIESLFSA FSNPAILRAE IRRLFDWLKE RGLTTVITAE ...String: GAMGIGKSPT GIQGFDELTL GGLPTGRPSL VCGSAGCGKT LFASTFLING VRDHGEPGVF VTFEERPEDI VNNVASLGFE LDKLIEEEKI AIEHIAVDPS EVAEIGDYDL EGLFLRLELA IDTVGAKRVV LDTIESLFSA FSNPAILRAE IRRLFDWLKE RGLTTVITAE RGDGALTRQG LEEYVSDCVI LLDHRVENQI STRRLRIVKY RGTAHGTNEY PFLIDTDGFS VLPVSALGLL HQVHEERIAS GVPDLDAMMA GGGFFRGSSI LVSGVAGAGK SSLAAHFAAA ACARGERAMY FSFEEAADQA VRNMRSLGLD LGRWRDAGLL RFMATRPTFY SLEMHLAVIL REVMRFEPSV VVLDPISAFT ESGDRLEVQS MLLRIVDFLK NRGITGIFTH LAHSQNEATT DAGLEELMDG WVLMLNREVN GEFNRELYLL KARGMAHSNQ VREFLMSDRG ISLLPPHLGE GGALTGTARK AEEARLRRAE IERQTELGRL QQQIEQRRRR ARAQIEALEA ELQAEEIALK ALVESESAHE RQRLADADTL ARSRGNERFA DLLMNKGE |
-Macromolecule #2: KaiB-RS
Macromolecule | Name: KaiB-RS / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAMGRRLVLY VAGQTPKSLA AISNLRRICE ENLPGQYEVE VIDLKQNPRL AKEHSIVAIP TLVRELPVPI RKIIGDLSDK EQVLVNLKMD ME |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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