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- EMDB-64812: Phycobilisome Rx rod from Gloeobacter violaceus PCC 7421 -

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Basic information

Entry
Database: EMDB / ID: EMD-64812
TitlePhycobilisome Rx rod from Gloeobacter violaceus PCC 7421
Map data
Sample
  • Complex: Bundle-shaped phycobilisome
    • Protein or peptide: Glr2806 protein
    • Protein or peptide: Phycocyanin alpha chain
    • Protein or peptide: Phycocyanin beta chain
  • Ligand: PHYCOCYANOBILIN
KeywordsPhycobilisome / PHOTOSYNTHESIS
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Phycocyanin beta chain / Phycocyanin alpha chain / Glr2806 protein
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 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_64812.png

Downloads & links

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Map

FileDownload / File: emd_64812.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 256 pix.
= 320. Å		1.25 Å/pix.
x 256 pix.
= 320. Å		1.25 Å/pix.
x 256 pix.
= 320. 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-1.8271594 - 3.0025425
Average (Standard dev.)0.010125756 (±0.07638853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64812_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64812_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: Glr2806 protein
    • Protein or peptide: Phycocyanin alpha chain
    • Protein or peptide: Phycocyanin beta chain
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Bundle-shaped phycobilisome

SupramoleculeName: Bundle-shaped phycobilisome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)

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Macromolecule #1: Glr2806 protein

MacromoleculeName: Glr2806 protein / type: protein_or_peptide / ID: 1 / 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 #2: Phycocyanin alpha chain

MacromoleculeName: Phycocyanin alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 17.679852 KDa
SequenceString:
MKTVITEVIA SADSQGRFLN NTELQAANGR FQRATASMEA ARALTSNADS LVKGAVQEVY NKFPYLTQPG QMGYGDTNQA KCARDISHY LRFITYSLVA GGTGPLDDYI VAGLREVNRT FNLSPSWYIE ALKHIKGKVG SQLSGQPLTE ANAYIDYCIN A LS

UniProtKB: Phycocyanin alpha chain

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Macromolecule #3: Phycocyanin beta chain

MacromoleculeName: Phycocyanin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Molecular weightTheoretical: 18.478953 KDa
SequenceString:
MQDAFTKAIV AADLRGSFLS EQELNQLTNL VKESNKRLDA VNAITGNAAE IISDAAHKLF AEQTDLIRPG GNAYPNRRMA ACLRDMEII LRYVSYALLA GDASVLEDRC LNGLKETYVA LGTPTRSVAR AVQLMKETAI GYVNSPSGVT RGDCSALVNE A ATYFDKAA ASIA

UniProtKB: Phycocyanin beta chain

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Macromolecule #4: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 4 / Number of copies: 18 / 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: 2.72 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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