9W7K | pdb_00009w7k

Cryo-EM structure of CpcL-PBS2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural insight of a photosystem I-CpcL-phycobilisome supercomplex from a cyanobacterium Anabaena sp. PCC 7120.

Mao, Z.Li, Z.Li, X.Shen, L.Kuang, T.Wang, W.Shen, J.R.Han, G.

(2026) Proc Natl Acad Sci U S A 123: e2530459123-e2530459123

  • DOI: https://doi.org/10.1073/pnas.2530459123
  • Primary Citation Related Structures: 
    9W4J, 9W7K, 9WD5

  • PubMed 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 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 Anabaena 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.


  • Organizational Affiliation
    • State Key Laboratory of Forage Breeding-by-Design and Utilization, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I-associated linker protein CpcLA [auth 1]191Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P29988 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Go to UniProtKB:  P29988
Entity Groups  
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UniProt GroupP29988
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rodB [auth 2],
C [auth 3]
285Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P07123 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P07123 
Go to UniProtKB:  P07123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07123
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit162Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P07121 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P07121 
Go to UniProtKB:  P07121
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UniProt GroupP07121
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit172Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P07120 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore P07120 
Go to UniProtKB:  P07120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07120
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
AB [auth R]
BA [auth 1]
BB [auth R]
CA [auth 2]
CB [auth S]
AB [auth R],
BA [auth 1],
BB [auth R],
CA [auth 2],
CB [auth S],
DA [auth 3],
DB [auth T],
EA [auth 3],
EB [auth U],
FA [auth B],
FB [auth V],
GA [auth C],
GB [auth V],
HA [auth C],
HB [auth W],
IA [auth D],
IB [auth X],
JA [auth E],
JB [auth Y],
KA [auth E],
KB [auth Z],
LA [auth F],
MA [auth G],
NA [auth H],
OA [auth I],
PA [auth I],
QA [auth J],
RA [auth K],
SA [auth K],
TA [auth L],
UA [auth M],
VA [auth M],
WA [auth O],
XA [auth P],
YA [auth P],
ZA [auth Q]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONCoot

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-15
    Type: Initial release