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- EMDB-63605: chimera map of bundle-shaped phycobilisome with short rod from th... -

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Basic information

Entry
Database: EMDB / ID: EMD-63605
Titlechimera map of bundle-shaped phycobilisome with short rod from thylakoid-lacking cyanobacterium Gloeobacter violaceus PCC 7421
Map datachimera map of bundle-shaped phycobilisome with short rod from thylakoid-lacking cyanobacterium Gloeobacter violaceus PCC 7421
Sample
  • Complex: phycobilisome
Keywordsphycobilisome / light-harvesting complex / photosynthesis
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMa J / SUI S-F
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670745 China
National Natural Science Foundation of China (NSFC)31861143048 China
National Natural Science Foundation of China (NSFC)32000848 China
CitationJournal: Nat Commun / Year: 2025
Title: Light-induced structural adaptation of the bundle-shaped phycobilisome from thylakoid-lacking cyanobacterium Gloeobacter violaceus.
Authors: Jianfei Ma / Xin You / Shan Sun / Sen-Fang Sui /
Abstract: Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, ...Gloeobacter diverged from other lineages early in cyanobacterial evolution, preferentially growing under low light intensity conditions. Among cyanobacteria, G. violaceus exhibits unique features, including lack of a thylakoid membrane and bundle-shaped antenna phycobilisomes (PBSs), densely packed and well-organized on the plasma membrane. However, without high-resolution structures, it has remained unclear how G. violaceus PBSs assemble into a bundle-shaped configuration. Here we solve the cryo-EM structures of PBSs from G. violaceus cells cultured under low (Sr-PBS) or moderate (Lr-PBS) light intensity. These structures reveal two unique linker proteins, L and L, that play a key role in the PBS architecture. Analysis of the bilin arrangement indicates that the bundle-shaped structure allows efficient energy transfer among rods. Moreover, comparison between Lr-PBS and Sr-PBS uncovers a distinct mode of adaption to increased light intensity wherein the ApcA-ApcB-ApcD layer can be blocked from binding to the core by altering structural elements exclusively found in the G. violaceus L. This study illustrates previously unrecognized mechanisms of assembly and adaptation to varying light intensity in the bundle-shaped PBS of G. violaceus.
History
DepositionMar 2, 2025-
Header (metadata) releaseJan 7, 2026-
Map releaseJan 7, 2026-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63605.png

Downloads & links

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Map

FileDownload / File: emd_63605.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationchimera map of bundle-shaped phycobilisome with short rod from thylakoid-lacking cyanobacterium Gloeobacter violaceus PCC 7421
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 560 pix.
= 614.824 Å		1.1 Å/pix.
x 560 pix.
= 614.824 Å		1.1 Å/pix.
x 560 pix.
= 614.824 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.473043 - 3.070368
Average (Standard dev.)0.003897873 (±0.0860949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 614.82404 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : phycobilisome

EntireName: phycobilisome
Components
  • Complex: phycobilisome

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Supramolecule #1: phycobilisome

SupramoleculeName: phycobilisome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 7.0 MDa

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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:
ConcentrationFormulaName
0.75 mol/LNa2HPO4disodium hydrogen phosphate
0.75 mol/LKH2PO4Monobasic Potassium Phosphate
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 18 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsSpherical aberration corrector: Spherical aberration (Cs) corrector
Energy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 12420 / Average exposure time: 8.2 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1042622
CTF correctionSoftware - Name: CTFFIND (ver. 4.15) / Type: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 389430
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 130000 / Software - Name: RELION (ver. 3.1.3)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 31.63 / Target criteria: 0.9

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