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- EMDB-65635: Cryo-EM structure of CpcL-PBS3 -

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Basic information

Entry
Database: EMDB / ID: EMD-65635
TitleCryo-EM structure of CpcL-PBS3
Map data
Sample
  • Complex: CpcL-PBS3
    • Protein or peptide: Photosystem I-associated linker protein CpcL
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rod
  • Ligand: PHYCOCYANOBILIN
KeywordsPhycobilisomes / PHOTOSYNTHESIS
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
C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Photosystem I-associated linker protein CpcL / Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rod
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsMao ZY / Li ZH / Han GY
Funding support China, 1 items
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
DepositionJul 31, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65635.png

Downloads & links

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Map

FileDownload / File: emd_65635.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å		1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.30545858 - 0.86861044
Average (Standard dev.)0.00026933535 (±0.02439092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65635_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65635_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : CpcL-PBS3

EntireName: CpcL-PBS3
Components
  • Complex: CpcL-PBS3
    • Protein or peptide: Photosystem I-associated linker protein CpcL
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rod
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: CpcL-PBS3

SupramoleculeName: CpcL-PBS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: Photosystem I-associated linker protein CpcL

MacromoleculeName: Photosystem I-associated linker protein CpcL / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 22.399137 KDa
SequenceString: MALPLLEYKP TTQNQRVQSF GTADVNEDTP YIYRLENANS PSEIEELIWA AYRQVFNEQE ILKFNRQIGL ETQLKNRSIT VKDFIRGLA KSERFYQLVV TPNNNYRLVE MSLKRLLGRS PYNEEEKIAW SIQIASKGWG GFVDALIDST EYEQAFGDNT V PYQRKRLT ...String:
MALPLLEYKP TTQNQRVQSF GTADVNEDTP YIYRLENANS PSEIEELIWA AYRQVFNEQE ILKFNRQIGL ETQLKNRSIT VKDFIRGLA KSERFYQLVV TPNNNYRLVE MSLKRLLGRS PYNEEEKIAW SIQIASKGWG GFVDALIDST EYEQAFGDNT V PYQRKRLT TDRPFSFTPR YGADYRDRAG IVRP

UniProtKB: Photosystem I-associated linker protein CpcL

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Macromolecule #2: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 17.475451 KDa
SequenceString:
MVKTPITEAI AAADTQGRFL GNTELQSARG RYERAAASLE AARGLTSNAQ RLIDGATQAV YQKFPYTTQT PGPQFAADSR GKSKCARDV GHYLRIITYS LVAGGTGPLD EYLIAGLAEI NSTFDLSPSW YVEALKHIKA NHGLSGQAAN EANTYIDYAI N ALS

UniProtKB: C-phycocyanin alpha subunit

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Macromolecule #3: C-phycocyanin beta subunit

MacromoleculeName: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 18.403758 KDa
SequenceString:
MTLDVFTKVV SQADSRGEFL SNEQLDALAN VVKEGNKRLD VVNRITSNAS AIVTNAARAL FEEQPQLIAP GGNAYTNRRM AACLRDMEI ILRYVTYAIL AGDASVLDDR CLNGLRETYQ ALGTPGSSVA VGVQKMKDAA VGIANDPNGI TKGDCSQLIS E VASYFDRA AAAVG

UniProtKB: C-phycocyanin beta subunit

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Macromolecule #4: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 32.254086 KDa
SequenceString: MAITTAASRL GTEPFSDAPK VELRPKASRE EVESVIRAVY RHVLGNDYIL ASERLVSAES LLRDGNLTVR EFVRSVAKSE LYKKKFFYN SFQTRLIELN YKHLLGRAPY DESEVVYHLD LYQNKGYDAE IDSYIDSWEY QSNFGDNVVP YYRGFETQVG Q KTAGFNRI ...String:
MAITTAASRL GTEPFSDAPK VELRPKASRE EVESVIRAVY RHVLGNDYIL ASERLVSAES LLRDGNLTVR EFVRSVAKSE LYKKKFFYN SFQTRLIELN YKHLLGRAPY DESEVVYHLD LYQNKGYDAE IDSYIDSWEY QSNFGDNVVP YYRGFETQVG Q KTAGFNRI FRLYRGYANS DRAQVEGTKS RLARELASNK ASTIVGPSGT NDSWGFRASA DVAPKKNLGN AVGEGDRVYR LE VTGIRSP GYPSVRRSST VFIVPYERLS DKIQQVHKQG GKIVSVTSA

UniProtKB: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod

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Macromolecule #5: Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-ass...

MacromoleculeName: Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rod
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 7.233297 KDa
SequenceString:
AAPTLISSAT KGDNRMFVIE AIAGGLNTNV AVRRSRQVYT VSYERLSATY QEIHKRGGKI VKISQV

UniProtKB: Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rod

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Macromolecule #6: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 6 / Number of copies: 54 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 74453
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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