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- EMDB-64868: Phycobilisome from Gloeobacter violaceus PCC 7421,composite map -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-64868
TitlePhycobilisome from Gloeobacter violaceus PCC 7421,composite map
Map data
Sample
  • Complex: Bundle-shaped phycobilisome
KeywordsPhycobilisome / PHOTOSYNTHESIS
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsBurtseva AD / Baymukhametov TN / Slonimskiy YB / Popov VO / Sluchanko NN / Boyko KM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: To Be Published
Title: Structure and quenching of a bundle-shaped phycobilisome
Authors: Burtseva AD / Slonimskiy YB / Baymukhametov TN / Sinetova MA / Maksimov EG / Popov VO / Boyko KM / Sluchanko NN
History
DepositionMay 30, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64868.png

Downloads & links

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Map

FileDownload / File: emd_64868.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 672 pix.
= 840. Å		1.25 Å/pix.
x 672 pix.
= 840. Å		1.25 Å/pix.
x 672 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.00007761802 - 2.1667352
Average (Standard dev.)0.016224686 (±0.051964957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 840.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Bundle-shaped phycobilisome

EntireName: Bundle-shaped phycobilisome
Components
  • Complex: Bundle-shaped phycobilisome

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Supramolecule #1: Bundle-shaped phycobilisome

SupramoleculeName: Bundle-shaped phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl
Component - Name: Tris(hydroxymethyl)aminomethane hydrochloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 3.9 sec. / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 85000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: OTHER / Number images used: 3942504
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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