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

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Basic information

Database: EMDB / ID: 3603
TitleKaiCB circadian clock backbone model based on a Cryo-EM density
SampleKaiCB circadian clock complex
SourceSynechococcus elongatus / bacteria / cyanobacteria
Map dataCircadian Clock Complex KaiBC
Methodsingle particle reconstruction, at 7 Å resolution
AuthorsSchuller JM / Snijder J / Loessl P / Heck AJR / Foerster F
CitationScience, 2017, 355, 1181-1184

Science, 2017, 355, 1181-1184 Yorodumi Papers
Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state.
Joost Snijder / Jan M Schuller / Anika Wiegard / Philip Lössl / Nicolas Schmelling / Ilka M Axmann / Jürgen M Plitzko / Friedrich Förster / Albert J R Heck

DateDeposition: Feb 24, 2017 / Header (metadata) release: Mar 29, 2017 / Map release: Apr 12, 2017 / Last update: Jul 12, 2017

Structure visualization

  • 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
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


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

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

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


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0240.0370.000

Supplemental data

Sample components

Entire KaiCB circadian clock complex

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

Component #1: protein, KaiCB circadian clock complex

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

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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
CameraDetector: GATAN K2 (4k x 4k)

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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