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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
SampleKaiCB circadian clock complex
SourceSynechococcus elongatus / bacteria / cyanobacteria
Map dataCircadian Clock Complex KaiBC
Methodsingle particle reconstruction, at 7 A resolution
AuthorsSchuller JM / Snijder J / Loessl P / Heck AJR / Foerster F
CitationScience, 2017, 355, 1181-1184

Science, 2017, 355, 1181-1184 StrPapers
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: Feb 24, 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
  • Download
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Supplemental images

Downloads & links

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Map

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

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AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
1.35 A/pix
= 264.6 A
196 pix
1.35 A/pix
= 264.6 A
196 pix
1.35 A/pix
= 264.6 A

Surface

Projections

Slices (1/3)

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 A
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 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / bacteria / cyanobacteria
Source (engineered)Expression System: Synechococcus elongatus / bacteria / cyanobacteria

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Experimental details

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Sample preparation

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

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/A2 / 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 A / Resolution method: FSC 0.143 CUT-OFF

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