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- EMDB-31944: Pentacylindrical allophycocyanin core from Thermosynechococcus vu... -

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Basic information

Entry
Database: EMDB / ID: EMD-31944
TitlePentacylindrical allophycocyanin core from Thermosynechococcus vulcanus
Map dataCryo-EM map
Sample
  • Complex: Phycobilisome core complex from Thermosynechococcus vulcanus
    • Protein or peptide: Allophycocyanin alpha chain
    • Protein or peptide: Allophycocyanin beta chain
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Phycobilisome core component
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Ligand: PHYCOCYANOBILIN
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
Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE / Phycobilisome core component
Similarity search - Component
Biological speciesThermosynechococcus vulcanus NIES-2134 (bacteria) / Thermosynechococcus vestitus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKawakami K / Hamaguchi T / Hirose Y / Kosumi D / Miyata M / Kamiya N / Yonekura K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05109 Japan
Japan Society for the Promotion of Science (JSPS)20K06528 Japan
Japan Society for the Promotion of Science (JSPS)17H06434 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Authors: Keisuke Kawakami / Tasuku Hamaguchi / Yuu Hirose / Daisuke Kosumi / Makoto Miyata / Nobuo Kamiya / Koji Yonekura /
Abstract: Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are ...Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.
History
DepositionSep 8, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateAug 17, 2022-
Current statusAug 17, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31944.png

Downloads & links

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Map

FileDownload / File: emd_31944.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å		1.24 Å/pix.
x 300 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00612
Minimum - Maximum-0.15001369 - 0.24053703
Average (Standard dev.)0.00014635992 (±0.0060940995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Phycobilisome core complex from Thermosynechococcus vulcanus

EntireName: Phycobilisome core complex from Thermosynechococcus vulcanus
Components
  • Complex: Phycobilisome core complex from Thermosynechococcus vulcanus
    • Protein or peptide: Allophycocyanin alpha chain
    • Protein or peptide: Allophycocyanin beta chain
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Phycobilisome core component
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Phycobilisome core complex from Thermosynechococcus vulcanus

SupramoleculeName: Phycobilisome core complex from Thermosynechococcus vulcanus
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Thermosynechococcus vulcanus NIES-2134 (bacteria)

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Macromolecule #1: Allophycocyanin alpha chain

MacromoleculeName: Allophycocyanin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 17.555926 KDa
SequenceString:
MSVVTKSIVN ADAEARYLSP GELDRIKNFV STGERRLRIA QTLTENRERI VKQAGDQLFQ KRPDVVSPGG NAYGEEMTAT CLRDLDYYL RLVTYGIVAG DVTPIEEIGL VGVREMYNSL GTPIPAVAEG IRAMKNVACS LLSAEDAAEA GSYFDFVIGA M Q

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Macromolecule #2: Allophycocyanin beta chain

MacromoleculeName: Allophycocyanin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 17.388877 KDa
SequenceString:
MQDAITAVIN ASDVQGKYLD TAAMEKLKAY FATGELRVRA ASVISANAAN IVKEAVAKSL LYSDITRPGG (MEN)MYTTR RYA ACIRDLDYYL RYATYAMLAG DPSILDERVL NGLKETYNSL GVPIAATVQA IQAMKEVTAS LVGADAGKEM GIYFDYI CS GLS

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Macromolecule #3: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 127.772922 KDa
SequenceString: MVVKASGGSS VARPQLYQTV PVSTIIQAEQ QDRFLNRGEL DELAVYLRSG AKRLEIATTL TRNADIIVSR AANRIFVGGS PMAFLSRPQ TEEAPQFTTG ARGEAIDIKE AMKLGTATYV DTRGGFLEGL RSIFSASSGG APVGFKPINI ARYGPARMEK S LRDLDWFL ...String:
MVVKASGGSS VARPQLYQTV PVSTIIQAEQ QDRFLNRGEL DELAVYLRSG AKRLEIATTL TRNADIIVSR AANRIFVGGS PMAFLSRPQ TEEAPQFTTG ARGEAIDIKE AMKLGTATYV DTRGGFLEGL RSIFSASSGG APVGFKPINI ARYGPARMEK S LRDLDWFL RYTTYAIVAG DPNILAVNTR GLREIIEAAC SSDATIAALQ EMRRAALSYF EKDAEAKGIV ETYFDVLINE FI APAPSDK VRQRNSTDLQ GLQLPQIYFN AAERRPKFVM KPGLSAAEKN EVVKAAYRQI FERDISRAYG LGISDLESKV KNG SISMKE FIRQLAKSPL YRKNFYEPYI NSRALELAFR HILGRGPSSR EEVQTYFAII SKGGLPALVD ALVDSKEYSD YFGE ETVPY LRGLGQEAQE CRNWGAQQDL FKYSAPFRKV PQFITTFAAQ DQPLPDQHPY GSGNDPLEIQ FGAIFPKEKK NPSAR PQPF NKDTRRILIA RGPGINNQVS NPGARGLTPG TLGPKVFKLD QLPSINARIG KRSIATGTDS VKFAESSTQR VIRAAY LQV FGRDVYEGQR QKVAEIKLEN GEISVREFVR ILAKSNLFRS LYWTPLYVTK AIEYIHRRLL GRPTYGRQEM NAYFDIA SK KGLYGLVDAI IDSQEYSEAF GEDTVPYERY ITPQGLALRS LRVGTIGETG VPPEKEETPR FVELGAVTEL RTEPAIQF R ANQGVSKRRE QTKVFKLTDL NDKQNLQLVI QAAYRQVFER DVAPYIVRDE FTALESKLSN GEITLKEFIE ALGCSELYQ KEFYTPYPNT KVIELGTKHF LGRAPLDQAE IRRYNQILAT QGLKAFVQAL VSSAEYAQAF GEDTVPYRRF PTLPAANFPN TEKLHNQLT KQSDAIVVPS FAPVKPRLDN TKLPLLSRAI AEQEAKARQA DPSKPRFIEL GRSFRNGDGQ SVEVGVGTTR R RPARIFRM TVGAPSAEVE LVINAIYCQV MDVFSGQVPS QFRRPDLESR LRNGEITVRE FVRTLASSEI YRNRFYTPYP NT KVIEFLF RHLLGRAPAT QAEIRQYNKI LADQGLKTAV ETMVNSPEYS RYFGEDVVPY KRFPTLPAGN YIGSVKADAD LVK QSWSSL SPSLVGIQPS HRD

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Macromolecule #4: Phycobilisome core component

MacromoleculeName: Phycobilisome core component / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 18.757221 KDa
SequenceString:
MRDAVTTLIK NYDSTGRYLD RDAVDRLRSY FNSGAARVKA AAVINANAAA IVKEAASALF TEQPELIQPG G(MEN)AYTT RRY ATCLRDMDYY LRYASYAIVA GDVDVLNERV LEGLRETYNS LGVPIGPTVR GIQIMKEIVR DRVAAAGIED TGIVEQP FD YMCRQLSEVN I

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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: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 7.876255 KDa
SequenceString:
MRMFKITACV PSQTRIRTQR ELQNTYFTKL VPYENWFREQ QRIQKMGGKI VKVELFTGKP GVNTGLA

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Macromolecule #6: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 6 / Number of copies: 84 / 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: 6.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 84.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 25532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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