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- EMDB-65950: The structure of phycobilisome with a bicylindrical core from the... -

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Basic information

Entry
Database: EMDB / ID: EMD-65950
TitleThe structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942
Map data
Sample
  • Complex: the major light-harvesting complexes Phycobilisomes (PBSs)
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
KeywordsPBS / ELECTRON TRANSPORT
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / 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
Allophycocyanin, beta subunit / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome rod-core linker polypeptide / Phycobilisome rod linker polypeptide / Phycobilisome rod linker polypeptide / Phycobiliprotein ApcE / Allophycocyanin alpha chain / Allophycocyanin, beta subunit / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core ...Allophycocyanin, beta subunit / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Phycobilisome rod-core linker polypeptide / Phycobilisome rod linker polypeptide / Phycobilisome rod linker polypeptide / Phycobiliprotein ApcE / Allophycocyanin alpha chain / Allophycocyanin, beta subunit / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Uncharacterized protein / Allophycocyanin alpha-B chain
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng ZG / Ma CY / Wang HR / Wang GP / Dong CX / Gao N / Zhao JD
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Photosynth Res / Year: 2025
Title: The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942.
Authors: Zhenggao Zheng / Chengying Ma / Hongrui Wang / Guopeng Wang / Chunxia Dong / Ning Gao / Jindong Zhao /
Abstract: Phycobilisomes (PBSs) are the major light-harvesting complexes in the cyanobacteria and red algae and they consist of a central core and peripheral rods that are attached to the core. The PBS cores ...Phycobilisomes (PBSs) are the major light-harvesting complexes in the cyanobacteria and red algae and they consist of a central core and peripheral rods that are attached to the core. The PBS cores contain 2-5 allophycocyanin cylinders that are organized by ApcE. At the present, structures of PBS with tricylindrical and pentacylindrical cores have been determined while the structure of the PBS with a bicylindrical core is yet to be revealed. Here we report the cryo-EM structure of PBS with bicylindrical core from Synechococcus elongatus PCC 7942 (Synechococcus 7942) at an overall resolution of approximately 3 Å. Similar to the PBS with a tricylindrical core, six peripheral rods are attached to the core by the rod-core linker protein CpcG in the PBS of Synechococcus 7942 even though the core lacks the top AP cylinder, which is important for the attachment of peripheral rods to the tricylindrical cores. We found that the C-terminus of ApcE in the Synechococcus 7942 was involved in interacting with both CpcG and CpcB of a top peripheral rod, compensating for the absence of the top AP cylinder of the core and maintaining PBS stability. Analysis of the bilin distribution reveals that distance of excitation energy transfer from top peripheral rods to the terminal emitters is approximately 15% shorter compared to the PBS with tricylindrical cores. Although there are 30% fewer bilin chromophores in the Synechococcus 7942 PBS core compared with the tricylindrical core, the aromatic residue ring in the Synechococcus 7942 PBS core is conserved, supporting the suggestion that these aromatic residues from AP and linker proteins are critical to the energy transfer of PBS.
History
DepositionAug 23, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65950.png

Downloads & links

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Map

FileDownload / File: emd_65950.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 560 pix.
= 599.2 Å		1.07 Å/pix.
x 560 pix.
= 599.2 Å		1.07 Å/pix.
x 560 pix.
= 599.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.0 - 0.0855578
Average (Standard dev.)0.00043832883 (±0.0024877195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 599.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : the major light-harvesting complexes Phycobilisomes (PBSs)

EntireName: the major light-harvesting complexes Phycobilisomes (PBSs)
Components
  • Complex: the major light-harvesting complexes Phycobilisomes (PBSs)
    • Protein or peptide: Phycobilisome rod-core linker polypeptide
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome rod linker polypeptide
    • Protein or peptide: Phycobilisome rod linker polypeptide
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: ApcG
    • Protein or peptide: Allophycocyanin, beta subunit
    • Protein or peptide: Allophycocyanin alpha chain
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Allophycocyanin, beta subunit
    • Protein or peptide: Allophycocyanin alpha-B chain
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: the major light-harvesting complexes Phycobilisomes (PBSs)

SupramoleculeName: the major light-harvesting complexes Phycobilisomes (PBSs)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)

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Macromolecule #1: Phycobilisome rod-core linker polypeptide

MacromoleculeName: Phycobilisome rod-core linker polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 28.372934 KDa
SequenceString: MALPLLNYAP TTQNSRVAGF EVPGDEQPKQ YNTEDQYSPV QFDEVIQAAY RQIFFHAFKC DRQTVLESQL RNGQITVRDF IRGLLLSAT FRSSFYDKNS NYRFVEQVVQ RVLGRDVYGE REKIAWSLAV ATQGYEGFID TLLNSDEYLS NFGYDKVPYQ R RRVLPGRA ...String:
MALPLLNYAP TTQNSRVAGF EVPGDEQPKQ YNTEDQYSPV QFDEVIQAAY RQIFFHAFKC DRQTVLESQL RNGQITVRDF IRGLLLSAT FRSSFYDKNS NYRFVEQVVQ RVLGRDVYGE REKIAWSLAV ATQGYEGFID TLLNSDEYLS NFGYDKVPYQ R RRVLPGRA LGETPFNIKS PRYDSYYRTI LGFPKAVFAG GPGKRFPAQY LSAKAGDPGA YLALARSIGA RGQALSASAD ID YLSKVPY RKR

UniProtKB: Phycobilisome rod-core linker polypeptide

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Macromolecule #2: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 72 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 17.303238 KDa
SequenceString:
MSKTPLTEAV AAADSQGRFL SSTELQVAFG RFRQAASGLA AAKALANNAD SLVNGAANAV YSKFPYTTST PGNNFASTPE GKAKCARDI GYYLRIVTYA LVAGGTGPID EYLLAGLDEI NKTFDLAPSW YVEALKYIKA NHGLSGDSRD EANSYIDYLI 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: 72 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 18.287713 KDa
SequenceString:
MTFDAFTKVV AQADARGEFL SDAQLDALSR LVAEGNKRID TVNRITGNAS SIVANAARAL FAEQPSLIAP GGNAYTNRRM AACLRDMEI ILRYVTYAVF TGDASILDDR CLNGLRETYL ALGVPGASVA EGVRKMKDAA VAIVSDRNGI TQGDCSAIIS E LGSYFDKA AAAVA

UniProtKB: C-phycocyanin beta subunit

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Macromolecule #4: Phycobilisome rod linker polypeptide

MacromoleculeName: Phycobilisome rod linker polypeptide / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 30.420775 KDa
SequenceString: MTSLEAARRL GFSAYSESAP LEWRAGASSD EINAIIRAVY RQVLGNDYVM GTERLTSAES LLRGGEISVR DFVRAVALSE LYREKFFHN NAHNRFIELN FKHLLGRAPY DQAEVAAHAA TYHSHGYDAD INSYIDSAEY TESFGDNVVP YFRGFATIRA Q KTVGFNRI ...String:
MTSLEAARRL GFSAYSESAP LEWRAGASSD EINAIIRAVY RQVLGNDYVM GTERLTSAES LLRGGEISVR DFVRAVALSE LYREKFFHN NAHNRFIELN FKHLLGRAPY DQAEVAAHAA TYHSHGYDAD INSYIDSAEY TESFGDNVVP YFRGFATIRA Q KTVGFNRI FQLYRGYATS DRSATSQRSR LDQEVARNAA SPVLIGSTDS ALVGTCGGSR DQLFRVQVQQ QGVTARTSNR IR RSNATYF VSYEKLNATL QRVHAQGGRI VSITPA

UniProtKB: Phycobilisome rod linker polypeptide

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Macromolecule #5: Phycobilisome rod linker polypeptide

MacromoleculeName: Phycobilisome rod linker polypeptide / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 31.734639 KDa
SequenceString: MAITVASSRL GTAPFSNAAP VELRPDGDRD QVQAVIRAVY RQVLGNDYIM KSERLTAAES LLVNGSISVR DFVRAVAKSE LYKTKFFYN NFQTRVIELH CKHLLGRAPY SEAEVIEHLD RYETQGYDAD VDSYIDSSEY LETFGESIVP YYRDIEYHVG Q QSVGLPRL ...String:
MAITVASSRL GTAPFSNAAP VELRPDGDRD QVQAVIRAVY RQVLGNDYIM KSERLTAAES LLVNGSISVR DFVRAVAKSE LYKTKFFYN NFQTRVIELH CKHLLGRAPY SEAEVIEHLD RYETQGYDAD VDSYIDSSEY LETFGESIVP YYRDIEYHVG Q QSVGLPRL FSLYRGYATS DRTSLGGNNS RLAANLAAKS VAPVVAPSVG TNYVASTKGE APMRALGGST PFGQTASRIF RV EIAAISK PGFPSVRRSN RSLLVPYEQL NNTLQQVNRS GGRVVSVAPA SL

UniProtKB: Phycobilisome rod linker polypeptide

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Macromolecule #6: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 7.821201 KDa
SequenceString:
MRMFRITACL PSPSKIRTQR ELQNTFFTKL VPYDAWFREQ QRIQKLGGKI IKVELATGRP NTNTGLL

UniProtKB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

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Macromolecule #7: ApcG

MacromoleculeName: ApcG / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 11.365804 KDa
SequenceString:
MVLDKLFGKK EKFFLEIDSS AASTETAAVE TAVTPVAAAV ETPTAAAGVA TPEPAATPAP EPVAEETPAK EIPNVTFAAD LSVPTINTG RRLPGPSLDP FVQIASEVVR R

UniProtKB: Uncharacterized protein

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Macromolecule #8: Allophycocyanin, beta subunit

MacromoleculeName: Allophycocyanin, beta subunit / type: protein_or_peptide / ID: 8 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 17.408725 KDa
SequenceString:
MQDAITAVIN ASDVQGKYLD SSALDRLKSY FQSGELRVRA AATISANSAL IVKEAVAKSL LYSDITRPGG NMYTTRRYAA CIRDLEYYL RYATYAMLAG DTSILDERVL NGLKETYNSL GVPIGATVQA IQAIKEVTAS LVGPDAGREM GVYLDYISSG L S

UniProtKB: Allophycocyanin, beta subunit

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Macromolecule #9: Allophycocyanin alpha chain

MacromoleculeName: Allophycocyanin alpha chain / type: protein_or_peptide / ID: 9 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 17.439717 KDa
SequenceString:
MSIVSKSIVN ADAEARYLSP GELERIKTFV VGGDRRLRIA QTIAESRERI VKQAGNQLFQ KRPDVVSPGG NAYGEDMTAT CLRDLDYYL RLVTYGVVSG DITPIEEIGI VGVREMYKSL GTPIEAVAEG VRELKSAATA LLTGEDADEA GAYFDYVIGA L S

UniProtKB: Allophycocyanin alpha chain

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Macromolecule #10: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 78.910289 KDa
SequenceString: MTVTASGGSS LARPQLYQTV PGSTIVQAEQ QDRFPQQGEL RELSSYFQSG LKRLAIAEII TRNSDTIVSR AANRIFVGGS PLAYIERPK VDPRNLRSAE EQRAREAKLG TVTFVESSGG GGFFSGLTAA LGGAGAVRIP SGFRPINVAR YGPRNMQKSL R DMSWFLRY ...String:
MTVTASGGSS LARPQLYQTV PGSTIVQAEQ QDRFPQQGEL RELSSYFQSG LKRLAIAEII TRNSDTIVSR AANRIFVGGS PLAYIERPK VDPRNLRSAE EQRAREAKLG TVTFVESSGG GGFFSGLTAA LGGAGAVRIP SGFRPINVAR YGPRNMQKSL R DMSWFLRY ITYAIVAGDP NILVVNVRGL REIIEKACST PATLVALQDM RATSAGYFRN DPEAQQLVKD YFDVLIREFE AP TPSLKQR QRFAEDQQGL ALPQSYANAA ERRPKFVIKS TLSTVEKNEA IKAAYRQVFE RDITRAYSQK VSDLESKVKN GEI STKEFI RRLGKSPLYR QQFHDRFVNS RVIELAFRHF LGRGISSAEE FTRYFDLLSA KGFAALIDAL VDSQEYADYF GEET VPYLR GLGQEAQECR NWGVQQELFK YSAPFVKVPQ FVTLFGEYKQ PLLDQHPYGA GNDPLEIQFG AIFPSRTVNN RTNPA PFGK DTRRLLVSKG GVNNQVGSAA FQQSGTTPTK IFKLTQVAAG SSSIRSKSVG NPSIRQTEST TQAVIRAAYR QVFGRD LYE GQRLTVPEIK LENGEITVRE FVRQIAKSET FRKLYWNNLY VVKAVEYIHR RLLGRPTTGR AEINAYFDIS AKKGFYA LV DAILDSPEYI AAFGEDTVPY ERYITPKGLA LRSVRGLEAS EKVKASLRPA AGAQERRPEV GRR

UniProtKB: Phycobiliprotein ApcE

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Macromolecule #11: Allophycocyanin, beta subunit

MacromoleculeName: Allophycocyanin, beta subunit / type: protein_or_peptide / ID: 11 / Details: ApcF / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 18.590818 KDa
SequenceString:
MRDAVSSLIA GYDLAGKYLD RNAVDSLRAY FAEGNARVQA AEIINANAAS LVRDASAQLF EEVPELLRPG GNAYTTRRYS ACLRDLDYY LRYATYALVA GNTEVLDERV LQGLRETYTS LGVPSGPTVR GIAILRDRVR QLVEQAGISN AAFVEVPFDH L GRNLAEQD I

UniProtKB: Allophycocyanin, beta subunit

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Macromolecule #12: Allophycocyanin alpha-B chain

MacromoleculeName: Allophycocyanin alpha-B chain / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Molecular weightTheoretical: 18.149797 KDa
SequenceString:
MTIVSQVILK ADDELRYPSG GELKNITDFF KTGEQRLRIA QVLSDSEKKI VDQASRKLWQ RRPDFIAPGG NAYGQRQRAQ CLRDYGWYL RLITYGVLAG DKEPIESIGL LGAREMYNSL GVPLPGMAEA IRTLKEASLA LLSSADATVA APYFDFLIQG M ETI

UniProtKB: Allophycocyanin alpha-B chain

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Macromolecule #13: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 13 / Number of copies: 252 / 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 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: OTHER / Software - Name: UCSF ChimeraX / Number images used: 258722
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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