9W4J | pdb_00009w4j

Cryo-EM structure of CpcL-PBS3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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]192Nostoc 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
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UniProt GroupP29988
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit163Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P07121 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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Go to UniProtKB:  P07121
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UniProt GroupP07121
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit173Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P07120 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP07120
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rodN [auth 2],
NA [auth 3]
286Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P07123 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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UniProt GroupP07123
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rodMA [auth 4]66Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
UniProt
Find proteins for P31329 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
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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 J]
AC [auth a]
BB [auth K]
BC [auth b]
CB [auth K]
AB [auth J],
AC [auth a],
BB [auth K],
BC [auth b],
CB [auth K],
CC [auth c],
DB [auth L],
DC [auth c],
EB [auth M],
EC [auth d],
FB [auth M],
FC [auth e],
GB [auth 2],
GC [auth e],
HB [auth O],
HC [auth f],
IB [auth P],
IC [auth g],
JB [auth P],
JC [auth g],
KB [auth Q],
KC [auth h],
LB [auth R],
LC [auth i],
MB [auth R],
MC [auth i],
NB [auth S],
NC [auth j],
OA [auth 1],
OB [auth T],
OC [auth k],
PA [auth B],
PB [auth U],
PC [auth k],
QA [auth C],
QB [auth V],
RA [auth C],
RB [auth V],
SA [auth D],
SB [auth W],
TA [auth E],
TB [auth X],
UA [auth E],
UB [auth X],
VA [auth F],
VB [auth Y],
WA [auth G],
WB [auth Z],
XA [auth H],
XB [auth Z],
YA [auth I],
YB [auth N],
ZA [auth I],
ZB [auth a]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 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