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- EMDB-3603: KaiCB circadian clock backbone model based on a Cryo-EM density -

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Basic information

Entry
Database: EMDB / ID: 3603
TitleKaiCB circadian clock backbone model based on a Cryo-EM density
Map dataCircadian Clock Complex KaiBC
SampleKaiCB circadian clock complex:
Function / homologyKaiC domain / KaiC domain profile. / KaiB domain / KaiC / Thioredoxin-like superfamily / Circadian clock protein kinase KaiC / P-loop containing nucleoside triphosphate hydrolase / KaiC-like domain / KaiB domain / Circadian clock KaiC, bacteria ...KaiC domain / KaiC domain profile. / KaiB domain / KaiC / Thioredoxin-like superfamily / Circadian clock protein kinase KaiC / P-loop containing nucleoside triphosphate hydrolase / KaiC-like domain / KaiB domain / Circadian clock KaiC, bacteria / Circadian clock protein KaiB / regulation of phosphorelay signal transduction system / entrainment of circadian clock / negative regulation of circadian rhythm / negative regulation of phosphorylation / regulation of circadian rhythm / rhythmic process / circadian rhythm / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / magnesium ion binding / regulation of transcription, DNA-templated / transcription, DNA-templated / DNA binding / ATP binding / identical protein binding / plasma membrane / cytoplasm / Circadian clock protein kinase KaiC / Circadian clock protein KaiB
Function and homology information
SourceSynechococcus elongatus (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / 7 Å resolution
AuthorsSchuller JM / Snijder J / Loessl P / Heck AJR / Foerster F
CitationJournal: 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.
DateDeposition: Feb 24, 2017 / Header (metadata) release: Mar 29, 2017 / Map release: Apr 12, 2017 / Last update: Jul 12, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3603.map.gz (map file in CCP4 format, 30119 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
1.35 Å/pix.
= 264.6 Å
196 pix
1.35 Å/pix.
= 264.6 Å
196 pix
1.35 Å/pix.
= 264.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.0095 (by author), 0.0095 (movie #1):
Minimum - Maximum-0.024160026 - 0.037031062
Average (Standard dev.)0.0001429749 (0.001844588)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions196196196
Origin000
Limit195195195
Spacing196196196
CellA=B=C: 264.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z264.600264.600264.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.0240.0370.000

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Supplemental data

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Sample components

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Entire KaiCB circadian clock complex

EntireName: KaiCB circadian clock complex / Number of components: 1

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Component #1: protein, KaiCB circadian clock complex

ProteinName: KaiCB circadian clock complex / Recombinant expression: No
SourceSpecies: Synechococcus elongatus (Cyanobacteria)
Source (engineered)Expression System: Synechococcus elongatus (Cyanobacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5137
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF

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