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- EMDB-66296: The cryo-EM structure of PBS from Synechococcus elongatus PCC 7942 -

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Basic information

Entry
Database: EMDB / ID: EMD-66296
TitleThe cryo-EM structure of PBS from Synechococcus elongatus PCC 7942
Map data
Sample
  • Complex: the major light-harvesting complexes Phycobilisomes (PBSs)
KeywordsPBS / ELECTRON TRANSPORT / PHOTOSYNTHESIS
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsZheng ZG / Ma CY / Wang HR / Wang GP / Dong CX / Gao N / Zhao JD
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Photosynth Res / Year: 2025
Title: The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942.
Authors: Zhenggao Zheng / Chengying Ma / Hongrui Wang / Guopeng Wang / Chunxia Dong / Ning Gao / Jindong Zhao /
Abstract: Phycobilisomes (PBSs) are the major light-harvesting complexes in the cyanobacteria and red algae and they consist of a central core and peripheral rods that are attached to the core. The PBS cores ...Phycobilisomes (PBSs) are the major light-harvesting complexes in the cyanobacteria and red algae and they consist of a central core and peripheral rods that are attached to the core. The PBS cores contain 2-5 allophycocyanin cylinders that are organized by ApcE. At the present, structures of PBS with tricylindrical and pentacylindrical cores have been determined while the structure of the PBS with a bicylindrical core is yet to be revealed. Here we report the cryo-EM structure of PBS with bicylindrical core from Synechococcus elongatus PCC 7942 (Synechococcus 7942) at an overall resolution of approximately 3 Å. Similar to the PBS with a tricylindrical core, six peripheral rods are attached to the core by the rod-core linker protein CpcG in the PBS of Synechococcus 7942 even though the core lacks the top AP cylinder, which is important for the attachment of peripheral rods to the tricylindrical cores. We found that the C-terminus of ApcE in the Synechococcus 7942 was involved in interacting with both CpcG and CpcB of a top peripheral rod, compensating for the absence of the top AP cylinder of the core and maintaining PBS stability. Analysis of the bilin distribution reveals that distance of excitation energy transfer from top peripheral rods to the terminal emitters is approximately 15% shorter compared to the PBS with tricylindrical cores. Although there are 30% fewer bilin chromophores in the Synechococcus 7942 PBS core compared with the tricylindrical core, the aromatic residue ring in the Synechococcus 7942 PBS core is conserved, supporting the suggestion that these aromatic residues from AP and linker proteins are critical to the energy transfer of PBS.
History
DepositionSep 22, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66296.png

Downloads & links

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Map

FileDownload / File: emd_66296.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 560 pix.
= 599.2 Å		1.07 Å/pix.
x 560 pix.
= 599.2 Å		1.07 Å/pix.
x 560 pix.
= 599.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.03694774 - 0.07835172
Average (Standard dev.)0.000173488 (±0.0019424341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 599.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66296_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_66296_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 : the major light-harvesting complexes Phycobilisomes (PBSs)

EntireName: the major light-harvesting complexes Phycobilisomes (PBSs)
Components
  • Complex: the major light-harvesting complexes Phycobilisomes (PBSs)

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Supramolecule #1: the major light-harvesting complexes Phycobilisomes (PBSs)

SupramoleculeName: the major light-harvesting complexes Phycobilisomes (PBSs)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
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: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 33425
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

9wg7


Chain - Source name: PDB / Chain - Initial model type: experimental model

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