8HFQ

Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM and femtosecond spectroscopic studies provide mechanistic insight into the energy transfer in CpcL-phycobilisomes.

Zheng, L.Zhang, Z.Wang, H.Zheng, Z.Wang, J.Liu, H.Chen, H.Dong, C.Wang, G.Weng, Y.Gao, N.Zhao, J.

(2023) Nat Commun 14: 3961-3961

  • DOI: https://doi.org/10.1038/s41467-023-39689-7
  • Primary Citation of Related Structures:  
    8HFQ

  • PubMed Abstract: 

    Phycobilisomes (PBS) are the major light harvesting complexes of photosynthesis in the cyanobacteria and red algae. CpcL-PBS is a type of small PBS in cyanobacteria that transfers energy directly to photosystem I without the core structure. Here we report the cryo-EM structure of the CpcL-PBS from the cyanobacterium Synechocystis sp. PCC 6803 at 2.6-Å resolution. The structure shows the CpcD domain of ferredoxin: NADP + oxidoreductase is located at the distal end of CpcL-PBS, responsible for its attachment to PBS. With the evidence of ultrafast transient absorption and fluorescence spectroscopy, the roles of individual bilins in energy transfer are revealed. The bilin 1I β 82 2 located near photosystem I has an enhanced planarity and is the red-bilin responsible for the direct energy transfer to photosystem I.


  • Organizational Affiliation

    School of Life Sciences, Peking University, Beijing, 100871, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha subunit162Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: cpcAsll1578
UniProt
Find proteins for Q54715 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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UniProt GroupQ54715
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta subunit172Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: cpcBsll1577
UniProt
Find proteins for Q54714 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1KA [auth k]291Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: cpcC1sll1580
UniProt
Find proteins for P73203 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2LA [auth l]273Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: cpcC2sll1579
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ferredoxin--NADP reductaseMA [auth m]413Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: petHslr1643
EC: 1.18.1.2
UniProt
Find proteins for Q55318 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I-associated linker protein CpcLNA [auth n]249Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: cpcLcpcG2sll1471
UniProt
Find proteins for P74625 (Synechocystis sp. (strain PCC 6803 / Kazusa))
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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 I]
AC [auth Z]
BB [auth J]
BC [auth a]
CB [auth J]
AB [auth I],
AC [auth Z],
BB [auth J],
BC [auth a],
CB [auth J],
CC [auth b],
DB [auth K],
DC [auth b],
EB [auth L],
EC [auth c],
FB [auth L],
FC [auth d],
GB [auth M],
GC [auth d],
HB [auth N],
HC [auth e],
IB [auth N],
IC [auth f],
JB [auth O],
JC [auth f],
KB [auth P],
KC [auth g],
LB [auth P],
LC [auth h],
MB [auth Q],
MC [auth h],
NB [auth R],
NC [auth i],
OA [auth A],
OB [auth R],
OC [auth j],
PA [auth B],
PB [auth S],
PC [auth j],
QA [auth B],
QB [auth T],
RA [auth C],
RB [auth T],
SA [auth D],
SB [auth U],
TA [auth D],
TB [auth V],
UA [auth E],
UB [auth V],
VA [auth F],
VB [auth W],
WA [auth F],
WB [auth X],
XA [auth G],
XB [auth X],
YA [auth H],
YB [auth Y],
ZA [auth H],
ZB [auth Z]
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.64 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release