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- PDB-9w7k: Cryo-EM structure of CpcL-PBS2 -

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Basic information

Entry
Database: PDB / ID: 9w7k
TitleCryo-EM structure of CpcL-PBS2
Components
  • C-phycocyanin alpha subunit
  • C-phycocyanin beta subunit
  • Photosystem I-associated linker protein CpcL
  • Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
KeywordsPHOTOSYNTHESIS / Phycobilisomes
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker protein / Phycocyanin, alpha subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker protein / Phycocyanin, alpha subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / 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 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Photosystem I-associated linker protein CpcL
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsMao, Z.Y. / Li, Z.H. / Han, G.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural insight of a photosystem I-CpcL-phycobilisome supercomplex from a cyanobacterium sp. PCC 7120.
Authors: Zhiyuan Mao / Zhenhua Li / Xingyue Li / Liangliang Shen / Tingyun Kuang / Wenda Wang / Jian-Ren Shen / Guangye Han /
Abstract: Phycobilisomes (PBSs) are supramolecular pigment-protein complexes composed of phycobiliproteins and linker proteins, serving as the major light-harvesting complexes that capture and transfer light ...Phycobilisomes (PBSs) are supramolecular pigment-protein complexes composed of phycobiliproteins and linker proteins, serving as the major light-harvesting complexes that capture and transfer light energy to photosystem II (PSII) and photosystem I (PSI) in cyanobacteria and eukaryotic red algae. In cyanobacteria, a rod-type PBS that does not have a core is specifically connected to PSI by a linker protein CpcL to form a PSI-CpcL-PBS supercomplex. However, the mechanism of CpcL-PBS association to PSI remains unclear. Here, we report the cryoelectron microscopic structures of PSI-CpcL-PBS at 2.98 Å and CpcL-PBS at 2.93 Å resolution from a cyanobacterium sp. PCC 7120, respectively. CpcL-PBS is located on the stromal side of a PSI tetramer and exhibits a structure of three-layered PBS consisting of four linkers (CpcL, CpcC1, CpcC2, PecC) and 18 pairs of phycocyanin αβ monomers. The C-terminal transmembrane helix of CpcL inserts to the membrane and interacts with PsaA, PsaB, and PsaM of PSI at an interface I between two PSI monomers, enabling the formation of the PSI-CpcL-PBS supercomplex. The exact structure of protein subunits and arrangement of bilin and chlorophyll pigments are revealed, which provide a structural basis for the assembly of PSI-CpcL-PBS and possible excitation energy transfer pathways from antennas to PSI within this supercomplex, shedding light on the organization and attachment of CpcL-PBS in cyanobacterial thylakoids.
History
DepositionAug 6, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Photosystem I-associated linker protein CpcL
2: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
3: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
B: C-phycocyanin alpha subunit
C: C-phycocyanin beta subunit
D: C-phycocyanin alpha subunit
E: C-phycocyanin beta subunit
F: C-phycocyanin alpha subunit
G: C-phycocyanin beta subunit
H: C-phycocyanin alpha subunit
I: C-phycocyanin beta subunit
J: C-phycocyanin alpha subunit
K: C-phycocyanin beta subunit
L: C-phycocyanin alpha subunit
M: C-phycocyanin beta subunit
O: C-phycocyanin alpha subunit
P: C-phycocyanin beta subunit
Q: C-phycocyanin alpha subunit
R: C-phycocyanin beta subunit
S: C-phycocyanin alpha subunit
T: C-phycocyanin beta subunit
U: C-phycocyanin alpha subunit
V: C-phycocyanin beta subunit
W: C-phycocyanin alpha subunit
X: C-phycocyanin beta subunit
Y: C-phycocyanin alpha subunit
Z: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,10963
Polymers513,91627
Non-polymers21,19336
Water00
1


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

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Components

#1: Protein Photosystem I-associated linker protein CpcL / L-RC 27.2 / Phycobilisome rod-core linker polypeptide CpcG3


Mass: 22267.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P29988
#2: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod


Mass: 32122.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P07123
#3: Protein
C-phycocyanin alpha subunit


Mass: 17344.256 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P07121
#4: Protein
C-phycocyanin beta subunit


Mass: 18272.562 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
References: UniProt: P07120
#5: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: CpcL-PBS2 / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270378 / Symmetry type: POINT

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