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- EMDB-34529: Un-sharpened map of phycobilisome from Porphyridium purpureum und... -

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Basic information

Entry
Database: EMDB / ID: EMD-34529
TitleUn-sharpened map of phycobilisome from Porphyridium purpureum under low light
Map dataLow Light unsharpen map
Sample
  • Complex: Complex of phycobilisome from red alga P.purpureum.
Keywordsphycobilisome / Complex / PHOTOSYNTHESIS
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsSui SF / Ma JF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2020
Title: Structural basis of energy transfer in Porphyridium purpureum phycobilisome.
Authors: Jianfei Ma / Xin You / Shan Sun / Xiaoxiao Wang / Song Qin / Sen-Fang Sui /
Abstract: Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red ...Photosynthetic organisms have developed various light-harvesting systems to adapt to their environments. Phycobilisomes are large light-harvesting protein complexes found in cyanobacteria and red algae, although how the energies of the chromophores within these complexes are modulated by their environment is unclear. Here we report the cryo-electron microscopy structure of a 14.7-megadalton phycobilisome with a hemiellipsoidal shape from the red alga Porphyridium purpureum. Within this complex we determine the structures of 706 protein subunits, including 528 phycoerythrin, 72 phycocyanin, 46 allophycocyanin and 60 linker proteins. In addition, 1,598 chromophores are resolved comprising 1,430 phycoerythrobilin, 48 phycourobilin and 120 phycocyanobilin molecules. The markedly improved resolution of our structure compared with that of the phycobilisome of Griffithsia pacifica enabled us to build an accurate atomic model of the P. purpureum phycobilisome system. The model reveals how the linker proteins affect the microenvironment of the chromophores, and suggests that interactions of the aromatic amino acids of the linker proteins with the chromophores may be a key factor in fine-tuning the energy states of the chromophores to ensure the efficient unidirectional transfer of energy.
History
DepositionOct 21, 2022-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34529.png

Downloads & links

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Map

FileDownload / File: emd_34529.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow Light unsharpen map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 560 pix.
= 610.96 Å		1.09 Å/pix.
x 560 pix.
= 610.96 Å		1.09 Å/pix.
x 560 pix.
= 610.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.017515415 - 0.0438318
Average (Standard dev.)-0.00010051873 (±0.002942202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 610.95996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Low Light unsharpen map half2

Fileemd_34529_half_map_1.map
AnnotationLow Light unsharpen map_half2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Low Light unsharpen map half1

Fileemd_34529_half_map_2.map
AnnotationLow Light unsharpen map_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 : Complex of phycobilisome from red alga P.purpureum.

EntireName: Complex of phycobilisome from red alga P.purpureum.
Components
  • Complex: Complex of phycobilisome from red alga P.purpureum.

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Supramolecule #1: Complex of phycobilisome from red alga P.purpureum.

SupramoleculeName: Complex of phycobilisome from red alga P.purpureum. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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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

Concentration1.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
750.0 mmol.L-1Na2HPO3Na2HPO3
750.0 mmol.L-1KH2PO3KH2PO3
Sugar embeddingMaterial: ice
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 16218 / Average exposure time: 5.6 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
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: 686369
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5y6p

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 157785
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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