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- PDB-9x6d: The cryo-EM structure of phycobilisome rod from Synechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 9x6d
TitleThe cryo-EM structure of phycobilisome rod from Synechococcus elongatus PCC 7942
Components
  • (C-phycocyanin ...) x 2
  • (Phycobilisome rod linker ...) x 2
  • Phycobilisome rod-core linker polypeptide
KeywordsELECTRON TRANSPORT / phycobilisome PBS
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome rod-core linker polypeptide / Phycobilisome rod linker polypeptide / Phycobilisome rod linker polypeptide
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsZheng, Z.G. / Ma, C.Y. / Wang, H.R. / Wang, G.P. / Dong, C.X. / Gao, N. / Zhao, J.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionOct 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycobilisome rod-core linker polypeptide
B: C-phycocyanin alpha subunit
C: C-phycocyanin beta subunit
D: C-phycocyanin beta subunit
E: C-phycocyanin beta subunit
F: C-phycocyanin alpha subunit
G: C-phycocyanin alpha subunit
H: C-phycocyanin alpha subunit
I: C-phycocyanin alpha subunit
J: C-phycocyanin beta subunit
K: C-phycocyanin alpha subunit
L: C-phycocyanin beta subunit
M: C-phycocyanin beta subunit
N: C-phycocyanin alpha subunit
O: C-phycocyanin beta subunit
P: C-phycocyanin beta subunit
Q: C-phycocyanin beta subunit
R: C-phycocyanin alpha subunit
S: C-phycocyanin alpha subunit
T: C-phycocyanin alpha subunit
U: C-phycocyanin alpha subunit
V: C-phycocyanin beta subunit
W: C-phycocyanin alpha subunit
X: C-phycocyanin beta subunit
Y: Phycobilisome rod linker polypeptide
Z: Phycobilisome rod linker polypeptide
a: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)537,60761
Polymers517,59227
Non-polymers20,01634
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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C-phycocyanin ... , 2 types, 24 molecules BFGHIKNRSTUWCDEJLMOPQVXa

#2: Protein
C-phycocyanin alpha subunit


Mass: 17303.238 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: P13530
#3: Protein
C-phycocyanin beta subunit


Mass: 18287.713 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: P06539

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Phycobilisome rod linker ... , 2 types, 2 molecules YZ

#4: Protein Phycobilisome rod linker polypeptide


Mass: 30392.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31PE0
#5: Protein Phycobilisome rod linker polypeptide


Mass: 31734.639 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31PD9

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Protein / Non-polymers , 2 types, 35 molecules A

#1: Protein Phycobilisome rod-core linker polypeptide


Mass: 28372.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
References: UniProt: Q31LK9
#6: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C33H40N4O6

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The rod of phycobilisome / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.19.2_4158model refinement
5RELIONCTF correction
13RELION3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 258722 / Symmetry type: POINT
RefinementHighest resolution: 2.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00536275
ELECTRON MICROSCOPYf_angle_d0.66449377
ELECTRON MICROSCOPYf_dihedral_angle_d11.49813173
ELECTRON MICROSCOPYf_chiral_restr0.0375534
ELECTRON MICROSCOPYf_plane_restr0.0036390

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