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Yorodumi- PDB-7x1y: Structure of the phosphorylation-site double mutant S431A/T432A o... -
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-Basic information
Entry | Database: PDB / ID: 7x1y | ||||||
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Title | Structure of the phosphorylation-site double mutant S431A/T432A of the KaiC circadian clock protein | ||||||
Components | Circadian clock oscillator protein KaiC | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / mutant | ||||||
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 / 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 | Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Han, X. / Zhang, D.L. / Hong, L. / Yu, D.Q. / Wu, Z.L. / Yang, T. / Rust, M.J. / Tu, Y.H. / Ouyang, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex Authors: Han, X. / Zhang, D. / Hong, L. / Yu, D. / Wu, Z. / Yang, T. / Rust, M. / Tu, Y. / Ouyang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x1y.cif.gz | 477.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x1y.ent.gz | 396.9 KB | Display | PDB format |
PDBx/mmJSON format | 7x1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x1y_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7x1y_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7x1y_validation.xml.gz | 84.9 KB | Display | |
Data in CIF | 7x1y_validation.cif.gz | 124.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/7x1y ftp://data.pdbj.org/pub/pdb/validation_reports/x1/7x1y | HTTPS FTP |
-Related structure data
Related structure data | 32952MC 7x1zC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 52757.922 Da / Num. of mol.: 6 / Mutation: S431A, T432A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 / Gene: kaiC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q79PF4 #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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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: KaiC hexamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Strain: PCC 7942 |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140475 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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