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- PDB-8hfq: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s... -

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Basic information

Entry
Database: PDB / ID: 8hfq
TitleCryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
Components
  • (C-phycocyanin ...) x 2
  • (Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod ...) x 2
  • Ferredoxin--NADP reductase
  • Photosystem I-associated linker protein CpcL
KeywordsPHOTOSYNTHESIS / CpcL-phycobilisome / energy transfer / ferredoxin:NADP+ oxidoreductase / ultrafast spectroscopy
Function / homology
Function and homology information


ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / 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 / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Phycocyanin, beta subunit / Ferredoxin--NADP reductase / CpcD-like domain ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Phycocyanin, beta subunit / Ferredoxin--NADP reductase / 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 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 / Photosystem I-associated linker protein CpcL / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsZheng, L. / Zhang, Z. / Wang, H. / Zheng, Z. / Gao, N. / Zhao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM and femtosecond spectroscopic studies provide mechanistic insight into the energy transfer in CpcL-phycobilisomes.
Authors: Lvqin Zheng / Zhengdong Zhang / Hongrui Wang / Zhenggao Zheng / Jiayu Wang / Heyuan Liu / Hailong Chen / Chunxia Dong / Guopeng Wang / Yuxiang Weng / Ning Gao / Jindong Zhao /
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 ...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 β located near photosystem I has an enhanced planarity and is the red-bilin responsible for the direct energy transfer to photosystem I.
History
DepositionNov 11, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 8, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_entry_details ...em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
C: C-phycocyanin alpha subunit
D: C-phycocyanin beta subunit
E: C-phycocyanin alpha subunit
F: C-phycocyanin beta subunit
G: C-phycocyanin alpha subunit
H: C-phycocyanin beta subunit
I: C-phycocyanin alpha subunit
J: C-phycocyanin beta subunit
K: C-phycocyanin alpha subunit
L: C-phycocyanin beta subunit
M: C-phycocyanin alpha subunit
N: 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
a: C-phycocyanin alpha subunit
b: C-phycocyanin beta subunit
c: C-phycocyanin alpha subunit
d: C-phycocyanin beta subunit
e: C-phycocyanin alpha subunit
f: C-phycocyanin beta subunit
g: C-phycocyanin alpha subunit
h: C-phycocyanin beta subunit
i: C-phycocyanin alpha subunit
j: C-phycocyanin beta subunit
k: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
l: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
m: Ferredoxin--NADP reductase
n: Photosystem I-associated linker protein CpcL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)813,56394
Polymers781,77340
Non-polymers31,78954
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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C-phycocyanin ... , 2 types, 36 molecules ACEGIKMOQSUWYacegiBDFHJLNPRTVX...

#1: Protein
C-phycocyanin alpha subunit


Mass: 17602.529 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: cpcA, sll1578 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q54715
#2: Protein
C-phycocyanin beta subunit


Mass: 18142.426 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: cpcB, sll1577 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q54714

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Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod ... , 2 types, 2 molecules kl

#3: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1


Mass: 32558.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: cpcC1, sll1580 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73203
#4: Protein Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 / LR30


Mass: 30836.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: cpcC2, sll1579 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73204

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Protein , 2 types, 2 molecules mn

#5: Protein Ferredoxin--NADP reductase / FNR


Mass: 46417.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: petH, slr1643 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55318, ferredoxin-NADP+ reductase
#6: Protein Photosystem I-associated linker protein CpcL / Phycobilisome rod-core linker polypeptide CpcG2


Mass: 28551.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: cpcL, cpcG2, sll1471 / Production host: Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74625

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Non-polymers , 1 types, 54 molecules

#7: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Synechocystis sp. PCC 6803 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124441 / Symmetry type: POINT

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