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- EMDB-52573: Structure of the bicylindrical allophycocyanin core expressed dur... -

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Basic information

Entry
Database: EMDB / ID: EMD-52573
TitleStructure of the bicylindrical allophycocyanin core expressed during far-red light photoacclimation (FaRLiP)
Map data
Sample
  • Complex: Bicylindrical far-red light adapted allophycocyanin complex
    • Protein or peptide: Phycocyanin
    • Protein or peptide: Allophycocyanin beta subunit apoprotein
    • Protein or peptide: Phycocyanin
    • Protein or peptide: Phycocyanin
    • Protein or peptide: Allophycocyanin beta-18 subunit apoprotein
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water
KeywordsPhycobilisome / Allophycocyanin / Complex / 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
Phycobiliprotein ApcE / Allophycocyanin beta subunit apoprotein / Phycocyanin / Phycocyanin / Phycocyanin / Allophycocyanin beta-18 subunit apoprotein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Similarity search - Component
Biological speciesChroococcidiopsis thermalis (bacteria) / Chroococcidiopsis thermalis PCC 7203 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsConsoli G / Leong HF / Davis GA / Richardson T / McInnes A / Murray JW / Fantuzzi A / Rutherford AW
Funding supportEuropean Union, United Kingdom, 6 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission955520European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Royal SocietyRoyal Society Research Professorship 2024 United Kingdom
CitationJournal: Commun Biol / Year: 2025
Title: Structure of a stripped-down and tuned-up far-red phycobilisome.
Authors: Giovanni Consoli / Ho Fong Leong / Geoffry A Davis / Tom Richardson / Aiysha McInnes / James W Murray / Andrea Fantuzzi / A William Rutherford /
Abstract: A diverse subset of cyanobacteria can transiently modify their photosynthetic machinery during far-red light photoacclimation to drive photosynthesis with less energetic photons (700 nm-800 nm). ...A diverse subset of cyanobacteria can transiently modify their photosynthetic machinery during far-red light photoacclimation to drive photosynthesis with less energetic photons (700 nm-800 nm). To achieve this, all the main light-driven components of the photosynthetic apparatus, including their allophycocyanin antenna, are replaced with red-shifted paralogues. Recent studies based on the structure of an incomplete complex provided some insights into the tuning of the far-red phycobiliproteins. Here, we solved the structure of the intact bicylindrical allophycocyanin complex from the cyanobacterium Chroococcidiopsis thermalis PCC 7203 at a resolution of 2.51 Å determined by Cryo-electron microscopy single particle analysis. A comparison between conserved structural features in far-red and white light allophycocyanin cores provides insight on the evolutionary adaptations needed to optimize excitation energy transfer in the far-red light adapted photosynthetic apparatus. The reduction in antenna size in far-red photosynthesis suggests a need to optimize membrane packing to increase the number of photosystems and tune the ratio between chlorophyll f molecules and bilin pigments, while the wider spread in the absorption range of the bilins suggests faster and more efficient excitation energy transfer to far-red Photosystem II by limiting backflow of excitation from the reaction centres to the far-red bilin pigments.
History
DepositionJan 16, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52573.png

Downloads & links

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Map

FileDownload / File: emd_52573.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 700 pix.
= 506.1 Å		0.72 Å/pix.
x 700 pix.
= 506.1 Å		0.72 Å/pix.
x 700 pix.
= 506.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.723 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6374968 - 1.4869522
Average (Standard dev.)0.002708527 (±0.04566609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 506.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52573_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_52573_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 : Bicylindrical far-red light adapted allophycocyanin complex

EntireName: Bicylindrical far-red light adapted allophycocyanin complex
Components
  • Complex: Bicylindrical far-red light adapted allophycocyanin complex
    • Protein or peptide: Phycocyanin
    • Protein or peptide: Allophycocyanin beta subunit apoprotein
    • Protein or peptide: Phycocyanin
    • Protein or peptide: Phycocyanin
    • Protein or peptide: Allophycocyanin beta-18 subunit apoprotein
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water

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Supramolecule #1: Bicylindrical far-red light adapted allophycocyanin complex

SupramoleculeName: Bicylindrical far-red light adapted allophycocyanin complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Chroococcidiopsis thermalis (bacteria)

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Macromolecule #1: Phycocyanin

MacromoleculeName: Phycocyanin / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 18.117572 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MSIVTELILN ADSESRYPAP KEIQVYQNFV KTGEQRIRIA KILAENEQRI VQNGSARFWE RVPNTPSNSG NERKTASCQR DQGWYIRLI AYSVLAGSEK PLEEIGTIGI KEMYNNLEIP LRNIVECMRC LKEEALSLMS EEDALEVSAY FDYVMRSLS

UniProtKB: Phycocyanin

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Macromolecule #2: Allophycocyanin beta subunit apoprotein

MacromoleculeName: Allophycocyanin beta subunit apoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 17.495893 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MQDAITALIN SSDVQGRYLD PSSLDKLQNY FQSGDMRAKT AIAVSANAKN IVTKTVAKSL LYTDITAPGG (MEN)MYTCR RYA ACVRDLDYFL RYATYAMLAG DTSILDERIL NGLRETYNSL GVPIGATIRS VQAMKEVVTS LVGADAGREM GVYFDHI AA GLS

UniProtKB: Allophycocyanin beta subunit apoprotein

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Macromolecule #3: Phycocyanin

MacromoleculeName: Phycocyanin / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 19.978068 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MSIVKQMILN ADEEVRYLTP GEIHALQNFY RSGTERIRLA KVLAQNEKKI VERATQKFWK ICPRTPSNSG NARKTEAAMR DIGWYIRLV SYCLLAGNEK PLEEIGLIGM KELYNSVGIP LENVRQYMLC VKAEVSAMLT PEDAAEVIPY FDLILQVISS P GAPYFQNN GRTDWQR

UniProtKB: Phycocyanin

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Macromolecule #4: Phycocyanin

MacromoleculeName: Phycocyanin / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 18.260959 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MSIITKAIAS ADREARYLSP GELRTIRDFY NGGENRLRIA TTLIENRKEI VERGSLKFWE CCPDTPSNSG NRTYRASCLR DQDWYIRLI AYTVIVGDVE PLKDIGIVGV KEMYESLEIP LRNWVECIRC LKEVTLDLLS REDAAEVTPY FDCLIQGMIP

UniProtKB: Phycocyanin

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Macromolecule #5: Allophycocyanin beta-18 subunit apoprotein

MacromoleculeName: Allophycocyanin beta-18 subunit apoprotein / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 18.777422 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MQDKLTSVAK NCDLTGSSLN REVVETLKEF LADGEKRVQV AGVIGSNAAE IVKTAVSLLF QEYPELVSPG G(MEN)AYTT RRY NMYVRDMNYF LRYCSYAIVA GDASVLDERL LAGLRDTFNS LGIPLGPTAR SIQLMKNIVK EKLVTAGMTN ITFVDEP FD YVVREISETE I

UniProtKB: Allophycocyanin beta-18 subunit apoprotein

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Macromolecule #6: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 88.103438 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString: MSVKASGGSP VTQPQRYHTV PVAVISHAVQ QDRCLKNTEL QELADFFSSG VKLLEIANTL TQHADEIVLA GANRIFVGGS PMAYLEKPK EKIGLPGSGY YVGEDFLTAA RRKAGAVMVK EALKIQEVAY YSNPLSGWLQ RFRDLFNNQD PLPGGFRFIN V SRYGAVRM ...String:
MSVKASGGSP VTQPQRYHTV PVAVISHAVQ QDRCLKNTEL QELADFFSSG VKLLEIANTL TQHADEIVLA GANRIFVGGS PMAYLEKPK EKIGLPGSGY YVGEDFLTAA RRKAGAVMVK EALKIQEVAY YSNPLSGWLQ RFRDLFNNQD PLPGGFRFIN V SRYGAVRM KRSMRDLAWF LRYITYAIVA GDGSILSANV RGLRGVIPED VTEATIVALR AMRRQSLDYF LEDAEATQLV KG YFDLLIA EYLTDKPSNQ VRIGVSNDQQ GLQLPQSYSM SAEVRPKFVF KQAATLTQKQ EAIAAIYRHV FERDVTDTYG FTQ KAELES QLIGGNISVK EFVRRLGKSR LYRRLFYEPF TISRAIELAA RHFLGRGLSS REEFQTYFDV MTKGGLPALV DAFV DSAEY SDYFGEETVP YLRGLGQEAQ ECRNWGPQLD LFKYSAPVRK VPQFITLFGS YQKPLPEQHP YGCGNDPLEI QFGAI FPQE TRNPHPQPAF FNKDTRRILI GSGAGSPDKL NGNALGKVPG SLGTRVLKLE PLHHANGKSN GVTQAGHQSP SVNLLH HSS PAFIEGAYRQ VFGRSLYEGQ RQPLSSTESK LLGGEISVRE FVRQLAKSKV FRSLYWDSLY VTKAIEYIHR RLMGRPT YG RQEMNRYYDI CATRGFYALI DAIIDSPEYL ECFGENTVPY ERYVTARGYL MRSPRHENQL RREQAAETVP DKYNPRKA N WAALTEFVEQ PILNQITSDG RSNRATEMRH AEIVGDRSNS PEESLEESYE YSQANDSER

UniProtKB: Phycobiliprotein ApcE

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Macromolecule #7: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 7.848333 KDa
Recombinant expressionOrganism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
SequenceString:
MRMFKVTACV PSQTRIRTQR ELQNTYFTKL VPYDNWFREQ QRIMKMGGKI VKVQLATGKP GMNTGLL

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

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Macromolecule #8: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 8 / Number of copies: 48 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 20 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.0 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
20.0 mMMeS
5.0 mMMgCl2
5.0 mMCaCl2
1.2 MBetaine
0.03 weight/volumeBeta-DM
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Detailsthe sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 9397 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36300
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8uhe


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9i1r:
Structure of the bicylindrical allophycocyanin core expressed during far-red light photoacclimation (FaRLiP)

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