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- EMDB-35552: Focused refinement cryo-EM map of D'1-D'2 cylinder in cyanobacter... -

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Basic information

Entry
Database: EMDB / ID: EMD-35552
TitleFocused refinement cryo-EM map of D'1-D'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster C-4, Map12)
Map data
Sample
  • Complex: cyanobacterial phycobilisome
KeywordsComplex / PHOTOSYNTHESIS
Biological speciesAnthocerotibacter panamensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsWang CH / Yang CH / Wu HY / Jiang HW / Ho MC / Ho MY
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: A structure of the relict phycobilisome from a thylakoid-free cyanobacterium.
Authors: Han-Wei Jiang / Hsiang-Yi Wu / Chun-Hsiung Wang / Cheng-Han Yang / Jui-Tse Ko / Han-Chen Ho / Ming-Daw Tsai / Donald A Bryant / Fay-Wei Li / Meng-Chiao Ho / Ming-Yang Ho /
Abstract: Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape ...Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a "paddle-shaped" PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
History
DepositionMar 4, 2023-
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_35552.png

Downloads & links

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Map

FileDownload / File: emd_35552.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 680 pix.
= 721.48 Å		1.06 Å/pix.
x 680 pix.
= 721.48 Å		1.06 Å/pix.
x 680 pix.
= 721.48 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-3.6554034 - 6.6709013
Average (Standard dev.)-0.00064874033 (±0.12196632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 721.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpen map

Fileemd_35552_additional_1.map
Annotationunsharpen map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35552_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35552_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cyanobacterial phycobilisome

EntireName: cyanobacterial phycobilisome
Components
  • Complex: cyanobacterial phycobilisome

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Supramolecule #1: cyanobacterial phycobilisome

SupramoleculeName: cyanobacterial phycobilisome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Anthocerotibacter panamensis (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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1109579
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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