+Open data
-Basic information
Entry | Database: PDB / ID: 5n8y | ||||||
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Title | KaiCBA circadian clock backbone model based on a Cryo-EM density | ||||||
Components |
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Keywords | TRANSFERASE / AAA+-ATPase / Kinase / Circadian Clock Complex / Cyanobacteria / Fold-switch | ||||||
Function / homology | Function and homology information detection of redox state / negative regulation of protein dephosphorylation / regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / negative regulation of phosphorylation / positive regulation of circadian rhythm / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm ...detection of redox state / negative regulation of protein dephosphorylation / regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / entrainment of circadian clock / negative regulation of phosphorylation / positive regulation of circadian rhythm / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm / circadian rhythm / non-specific serine/threonine protein kinase / phosphorylation / 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 / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Authors | Schuller, J.M. / Snijder, J. / Loessl, P. / Heck, A.J.R. / Foerster, F. | ||||||
Citation | Journal: Science / Year: 2017 Title: Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state. Authors: Joost Snijder / Jan M Schuller / Anika Wiegard / Philip Lössl / Nicolas Schmelling / Ilka M Axmann / Jürgen M Plitzko / Friedrich Förster / Albert J R Heck / Abstract: Cyanobacteria have a robust circadian oscillator, known as the Kai system. Reconstituted from the purified protein components KaiC, KaiB, and KaiA, it can tick autonomously in the presence of ...Cyanobacteria have a robust circadian oscillator, known as the Kai system. Reconstituted from the purified protein components KaiC, KaiB, and KaiA, it can tick autonomously in the presence of adenosine 5'-triphosphate (ATP). The KaiC hexamers enter a natural 24-hour reaction cycle of autophosphorylation and assembly with KaiB and KaiA in numerous diverse forms. We describe the preparation of stoichiometrically well-defined assemblies of KaiCB and KaiCBA, as monitored by native mass spectrometry, allowing for a structural characterization by single-particle cryo-electron microscopy and mass spectrometry. Our data reveal details of the interactions between the Kai proteins and provide a structural basis to understand periodic assembly of the protein oscillator. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5n8y.cif.gz | 642.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n8y.ent.gz | 439.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/5n8y ftp://data.pdbj.org/pub/pdb/validation_reports/n8/5n8y | HTTPS FTP |
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-Related structure data
Related structure data | 3602MC 3603C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 58072.773 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: kaiC, Synpcc7942_1216, see0011 / Production host: Escherichia coli (E. coli) References: UniProt: Q79PF4, non-specific serine/threonine protein kinase #2: Protein | Mass: 11450.387 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: kaiB, Synpcc7942_1217, see0010 / Production host: Escherichia coli (E. coli) / References: UniProt: Q79PF5 #3: Protein | Mass: 32666.199 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Gene: kaiA, Synpcc7942_1218, see0009 / Production host: Escherichia coli (E. coli) / References: UniProt: Q79PF6 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: KaiCBA circadian clock complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Synechococcus elongatus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 15.2 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32498 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |