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- EMDB-34534: Un-sharpened map of phycobilisome from Porphyridium purpureum und... -

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Basic information

Entry
Database: EMDB / ID: EMD-34534
TitleUn-sharpened map of phycobilisome from Porphyridium purpureum under Middle light
Map dataUn-sharpened map of phycobilisome under Middle light
Sample
  • Complex: phycobilisome
Keywordslight-harvesting complex / photosynthesis
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsMa JF / Sui S-F
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670745 China
National Natural Science Foundation of China (NSFC)31861143048 China
CitationJournal: Commun Biol / Year: 2023
Title: The structural basis for light acclimation in phycobilisome light harvesting systems systems in Porphyridium purpureum.
Authors: Emma Joy Dodson / Jianfei Ma / Maayan Suissa Szlejf / Naama Maroudas-Sklare / Yossi Paltiel / Noam Adir / Shan Sun / Sen-Fang Sui / Nir Keren /
Abstract: Photosynthetic organisms adapt to changing light conditions by manipulating their light harvesting complexes. Biophysical, biochemical, physiological and genetic aspects of these processes are ...Photosynthetic organisms adapt to changing light conditions by manipulating their light harvesting complexes. Biophysical, biochemical, physiological and genetic aspects of these processes are studied extensively. The structural basis for these studies is lacking. In this study we address this gap in knowledge by focusing on phycobilisomes (PBS), which are large structures found in cyanobacteria and red algae. In this study we focus on the phycobilisomes (PBS), which are large structures found in cyanobacteria and red algae. Specifically, we examine red algae (Porphyridium purpureum) grown under a low light intensity (LL) and a medium light intensity (ML). Using cryo-electron microscopy, we resolve the structure of ML-PBS and compare it to the LL-PBS structure. The ML-PBS is 13.6 MDa, while the LL-PBS is larger (14.7 MDa). The LL-PBS structure have a higher number of closely coupled chromophore pairs, potentially the source of the red shifted fluorescence emission from LL-PBS. Interestingly, these differences do not significantly affect fluorescence kinetics parameters. This indicates that PBS systems can maintain similar fluorescence quantum yields despite an increase in LL-PBS chromophore numbers. These findings provide a structural basis to the processes by which photosynthetic organisms adapt to changing light conditions.
History
DepositionOct 21, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34534.png

Downloads & links

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Map

FileDownload / File: emd_34534.map.gz / Format: CCP4 / Size: 744.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUn-sharpened map of phycobilisome under Middle light
Voxel sizeX=Y=Z: 1.066 Å
Density
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.013130775 - 0.03686599
Average (Standard dev.)0.00013427765 (±0.0024849707)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions580580580
Spacing580580580
CellA=B=C: 618.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Un-sharpened map of phycobilisome under Middle light half2

Fileemd_34534_half_map_1.map
AnnotationUn-sharpened map of phycobilisome under Middle light half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Un-sharpened map of phycobilisome under Middle light half1

Fileemd_34534_half_map_2.map
AnnotationUn-sharpened map of phycobilisome under Middle light half1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 / Macromolecule list: #1-#28
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 14700 kDa/nm

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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/LKH2PO4monopotassium phosphate
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / 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 TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum ER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 2 / Number real images: 6438 / 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: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 315046
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kgx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1beta) / Number images used: 87399
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1beta)
Final 3D classificationNumber classes: 5 / Avg.num./class: 87399 / Software - Name: RELION (ver. 3.1beta)

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Atomic model buiding 1

Initial modelPDB ID:

6kgx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 62.05 / Target criteria: 0,99

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