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- EMDB-64816: Phycobilisome allophycocyanin hexamer C from Gloeobacter violaceu... -

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Basic information

Entry
Database: EMDB / ID: EMD-64816
TitlePhycobilisome allophycocyanin hexamer C from Gloeobacter violaceus PCC 7421
Map data
Sample
  • Complex: Bundle-shaped phycobilisome
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Glr1262 protein
    • Protein or peptide: Allophycocyanin alpha subunit
    • Protein or peptide: Allophycocyanin beta subunit
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Glr2806 protein
  • Ligand: PHYCOCYANOBILIN
KeywordsPhycobilisome / PHOTOSYNTHESIS
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / 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
Glr2806 protein / Glr1262 protein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin beta subunit / Allophycocyanin alpha subunit / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsBurtseva AD / Baymukhametov TN / Slonimskiy YB / Popov VO / Sluchanko NN / Boyko KM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: Sci Adv / Year: 2025
Title: Structure and quenching of a bundle-shaped phycobilisome.
Authors: Anna D Burtseva / Yury B Slonimskiy / Timur N Baymukhametov / Maria A Sinetova / Daniil A Gvozdev / Georgy V Tsoraev / Dmitry A Cherepanov / Eugene G Maksimov / Vladimir O Popov / Konstantin ...Authors: Anna D Burtseva / Yury B Slonimskiy / Timur N Baymukhametov / Maria A Sinetova / Daniil A Gvozdev / Georgy V Tsoraev / Dmitry A Cherepanov / Eugene G Maksimov / Vladimir O Popov / Konstantin M Boyko / Nikolai N Sluchanko /
Abstract: Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in ...Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in high light. Among known PBS morphologies, the one from the basal cyanobacterial genus still lacks detailed structural characterization. Here, we reconstructed a cryo-electron microscopy structure of the >10-megadalton PBS, with diverging, conformationally mobile bundles of rods composed of stacked phycoerythrin and phycocyanin hexamers, stemming from a pentacylindrical allophycocyanin core belted by auxiliary phycocyanin hexamers. We show how two -specific multidomain linker proteins, Glr1262 and Glr2806, maintain this bundle-shaped architecture and reveal its differential regulation via nonphotochemical quenching by two OCP types of that recognize separate binding sites within the allophycocyanin core, including lateral cylinders absent in tricylindrical cores.
History
DepositionMay 28, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64816.png

Downloads & links

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Map

FileDownload / File: emd_64816.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 672 pix.
= 840. Å		1.25 Å/pix.
x 672 pix.
= 840. Å		1.25 Å/pix.
x 672 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.46778232 - 1.6037939
Average (Standard dev.)0.003017143 (±0.03696391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions672672672
Spacing672672672
CellA=B=C: 840.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64816_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_64816_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Bundle-shaped phycobilisome

EntireName: Bundle-shaped phycobilisome
Components
  • Complex: Bundle-shaped phycobilisome
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Glr1262 protein
    • Protein or peptide: Allophycocyanin alpha subunit
    • Protein or peptide: Allophycocyanin beta subunit
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Glr2806 protein
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Bundle-shaped phycobilisome

SupramoleculeName: Bundle-shaped phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)

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Macromolecule #1: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 130.002258 KDa
SequenceString: MSIRGTSGST VARPRLFRTV MTETINGINA EDRYPNSGEV SQLDQFFGDG QRRIAIVAKL TENAEMIVSR AANRIFVGGS PMAYSERQK AKAKSPLAND EFGNEPIVED RGGFLESLKS IFSTRGGGGR ASADFAVPPD FEPINIARYG PERMQKSIRD L DWFLRYTT ...String:
MSIRGTSGST VARPRLFRTV MTETINGINA EDRYPNSGEV SQLDQFFGDG QRRIAIVAKL TENAEMIVSR AANRIFVGGS PMAYSERQK AKAKSPLAND EFGNEPIVED RGGFLESLKS IFSTRGGGGR ASADFAVPPD FEPINIARYG PERMQKSIRD L DWFLRYTT YAILAGDPSI LEANCLGLRE ILEKSCSISA TIVALLEMRK NAARLFKDEA DSKLVSSYIS VVIRALDADR SD APADIVR PSSEDRPGLT LPYIYKLSAD SLTTFKMTAI YGADGRPKVN LSSDEKERVV RAAYRQVFER DLKAYGQSVS EAE SKVKNG EISVREFVRR LGKSELYRRE FYQPFINSRV LELAFKHFLG RAPESRAEVQ KYFSIISSPI VRGQSSMPSG GLYA LIDAL IDSEEYTSIF GEDTVPYLRN LGVEAQPSWN WGAAYDLYNY AAPRRKVPQF ITLFADYTQP LPNQHPYGAG NDPLE IQFG AIFKNSTINP AERAAPIGKD VKRILIRNGS PTSNERGNPT GMSEGATTLG PKIFKLTQNV GFRSKGMVQN AGVVTV EGS VQALITAAYQ QIFGRQLYQG QRLKVAEIKL ENGETTVKEF VRALGRSEIF RKLYWEPFYV CKAIEYIHRR LLGRPTY DR VENNRYFDIA SKKGFYGVVD AMLNSNEYQE VFGEDVLPYE RYLTPAGLSL RKGRFGSSDV LTTPGGITPR GDAARMMD K IQELGTPINE RSIPEMYVNQ GVPALKRQRK VFKQSQATDR ESFDALVTAA YVQVFDKDIA SYIRSEFSAL ESRLRNRET SVKEFVRLLG FSALYRKQFH DRYPNTKVVE FAFKHFLGRA VKNQAELIKY HGLLGRKGIK ALIGALVDGE EYGRLYGEDT VPSWQFPTL PAANYPNSVE LYNRFTRQDD SLVVPSFKPI RSKMDIASMP LVQAALKEQQ ATKTALDMSR PMFLELGRSF K GADGQSVE VGVGTLRRQL EHIYRIAPDA TRSEKDVAIN AIYRQVLDVF AGIPPSYLRL SEAESKLKNN EISVREFVRR LG RSENYRK RFFEPYSSPK VVELLTKHFL GRAPISQQEI STYVQILGTK GLAAAVDAIV ESPEYLTIFN EDIVPYRRYP TLP AGNYRA SVRVNDEELI SQSWSSLSPT YTGYQYVTR

UniProtKB: Phycobiliprotein ApcE

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Macromolecule #2: Glr1262 protein

MacromoleculeName: Glr1262 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 92.127602 KDa
SequenceString: MSTVLDDQSK AYAPGSANGP TAGLEPFVRM SRMIRSGVPE DREEPDELWL SMVRDIFGRG YMDRLSQTRA IDYSAFVRPA DQATADGAA QTKLGITAIA PDQGVELRPN FTEADVITVI RAAYKQLFGN TYILESERVI QAESLLRNGS ISVREFIRIL A KSDLYKER ...String:
MSTVLDDQSK AYAPGSANGP TAGLEPFVRM SRMIRSGVPE DREEPDELWL SMVRDIFGRG YMDRLSQTRA IDYSAFVRPA DQATADGAA QTKLGITAIA PDQGVELRPN FTEADVITVI RAAYKQLFGN TYILESERVI QAESLLRNGS ISVREFIRIL A KSDLYKER FFRCTSNNRF IELNLKHLLG RAPYNQGEIA EHLDRYCQSG YDAEIDSYID SDEYRRVFGE NTVPYFRGFK YQ VGQSAAA FERMRALYSG DAGSDTDRNQ NGQRTELTSG LADPAQPVRA RTDYALTRVD IPGGNGAAGR LAALDESLGS WLD AARDLI SQNDYSQKAI EVEPKRVAPY AQYLTPAVEA TPDAAAQTKL GITAVAPDQA VELRPNFGEA EVQAVIRAAY KQIF GNTYI LEADRVVIAE SLLRNGSISV REFVRLLAKS DLYRDRFFRT ASNNRFIELN FKHFLGRAPY SQAEIGEHFN RYHKS GYDA EIDSYIDSDE YRRVFGENTV PYFRGFKYQV GQAARGFDQM QQLFAGDAGS DTDRGIGAQP AAKLTFPLSR PLGVTS AYF PSSQGGAATS DGLEMFTRMA RELTVTPVSA RRTTSPTAPT APAMPLAGYY SRPAPRATAD GDAQTKLGIT AVAPAQA VE LRPNFGETEL QAVIRATYKQ LFGNTYILEA DRVVQAESLL RNGSINVREF VRLLAKSELY KERFFHCTSN NRFIELTF K HLLGRAPYNQ SEFVEHLDRY QKSGYDAEID SYIDSDEYRR VFGENTVPYF RGFKYQTGQA AGVFERTLKL YGGDADSDT NRNRQGQLRQ VDPQELLRSG RGIV

UniProtKB: Glr1262 protein

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Macromolecule #3: Allophycocyanin alpha subunit

MacromoleculeName: Allophycocyanin alpha subunit / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.555062 KDa
SequenceString:
MSVLTKAIVN ADAEARYLSP GELDRIKSFV ASGERRLRIA QTLTEARERI VKQAGDQLFQ KRPDVVSPGG NAYGEKMTAL CLRDLDYYL RLVTYGIVAG DVTPIEEIGI IGVKEMYNSL QTPIPAVAEG VRAMKNVATS LLSGDDAAEA GFYFDYLVGA M Q

UniProtKB: Allophycocyanin alpha subunit

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Macromolecule #4: Allophycocyanin beta subunit

MacromoleculeName: Allophycocyanin beta subunit / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.241664 KDa
SequenceString:
MQDAITAVIN NYDVQGKYLD GAALDKLKAY FTTGAVRVRA AAVISSNATT IIKEAAAKAL IYSDLTRPGG (MEN)MYTTR RYA ACIRDMDYFL RYATYAMLAG DPSILDERVL NGLKETYNSL GVPIAATVGG IQAMKEVVGG LVGPDAAKEA SIYFDYL SS GLS

UniProtKB: Allophycocyanin beta subunit

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Macromolecule #5: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 7.765004 KDa
SequenceString:
MSRYFKVTAC IPSLKRVRTG RELQNTFFTK LVPYENWFTE QQRIQKAGGK VLSVKLFTGV QGANTGVGA

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

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Macromolecule #6: Glr2806 protein

MacromoleculeName: Glr2806 protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 81.544312 KDa
SequenceString: MSATTYDWRK VIDSIKIEDP VKPGDFANFL DMARGIESRT GVWSISYESL RTLGPPEGGM LRPAVGGTAE AAAQKQLGIT AVAPASVVE LRPNASEEDL QGVLRAVYRQ VLGNTYVMES ERPTQAESLL RNGSISVREF VRRIAKSDLY KERFFNKASN N RFIELNFK ...String:
MSATTYDWRK VIDSIKIEDP VKPGDFANFL DMARGIESRT GVWSISYESL RTLGPPEGGM LRPAVGGTAE AAAQKQLGIT AVAPASVVE LRPNASEEDL QGVLRAVYRQ VLGNTYVMES ERPTQAESLL RNGSISVREF VRRIAKSDLY KERFFNKASN N RFIELNFK HLLGRAPYNH GEIQEHFGLY HKAGYDVEID SYIDSDEYIE TFGENIVPYF RGFKYQTNQS AGGFPRMVKL WG GDAGSDT DRGKNGQRTL VTTKDLIGPT KIFVPFVAPG RDADMVSGDY TRLAFGLSGE AAAQRQLGIA SVAPAPICQL RPN ASEEDL QGVLRAVYRQ VLGNTYVMES ERPTQAESLL RNGSISVREF VRRIAKSDLY KERFFNKASN NRFIELNFKH LLGR APYNH GEIQEHFGLY HKAGYDVEID SYIDSDEYIE TFGENIVPYF RGFKYQTNQS AGGFPRMVKL WGGDAGSDTD RATGG QRTL VTTRELVKTL PLLTEIPAVP ATRGFEQVLN QLKRPAPGGT GEAQGQKQLG ITAVAPAPIC QLRPNASEED LQGVLR AVY RQVLGNTYVM ESERPTQAES LLRNGSISVR EFVRRIAKSD LYKERFFNKA SNNRFIELNF KHLLGRAPYN HGEIQEH FG LYHKAGYDAE IDSYIDSDEY LLTFGEDVVP YFRGFKYQTN QSAGGFPRFT KLYGGDAGSD TDRGKNGQRT LVTTKDLV V SGQFSKPV

UniProtKB: Glr2806 protein

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Macromolecule #7: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 7 / Number of copies: 12 / 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 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl
Component - Name: Tris(hydroxymethyl)aminomethane hydrochloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average exposure time: 3.9 sec. / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 85000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 746972
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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