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- EMDB-42278: Structure of the far-red light-absorbing allophycocyanin core exp... -

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Basic information

Entry
Database: EMDB / ID: EMD-42278
TitleStructure of the far-red light-absorbing allophycocyanin core expressed during FaRLiP
Map dataFRL-AP core, sharpened and masked
Sample
  • Complex: Far-red light-absorbing allophycocyanin core
    • Protein or peptide: ApcD5
    • Protein or peptide: ApcB2
    • Protein or peptide: ApcD3
    • Protein or peptide: ApcD2
    • Protein or peptide: ApcF
    • Protein or peptide: ApcE2
    • Protein or peptide: ApcC
  • Ligand: PHYCOCYANOBILIN
  • Ligand: mesobiliverdin IX(alpha)
  • Ligand: CHLORIDE ION
Keywordslight-harvesting / allophycocyanin / phycocyanobilin / 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
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin, beta subunit / Phycobilisome protein / Phycobiliprotein ApcE / Phycobilisome protein / Allophycocyanin, beta subunit / Phycobilisome protein
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsGisriel CJ / Bryant DA / Brudvig GW / Shen G
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
CitationJournal: J Biol Chem / Year: 2024
Title: Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335.
Authors: Christopher J Gisriel / Gaozhong Shen / Gary W Brudvig / Donald A Bryant /
Abstract: Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths ...Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths typically used for oxygenic photosynthesis (400-700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment-protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.
History
DepositionOct 9, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42278.png

Downloads & links

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Map

FileDownload / File: emd_42278.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFRL-AP core, sharpened and masked
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 0.0198
Minimum - Maximum-0.11052769 - 0.11786466
Average (Standard dev.)0.00030532022 (±0.0043463754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: FRL-AP core, sharpened without mask

Fileemd_42278_additional_1.map
AnnotationFRL-AP core, sharpened without mask
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: FRL-AP core, unsharpened

Fileemd_42278_additional_2.map
AnnotationFRL-AP core, unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: FRL-AP core, half 2

Fileemd_42278_half_map_1.map
AnnotationFRL-AP core, half 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: FRL-AP core, half 1

Fileemd_42278_half_map_2.map
AnnotationFRL-AP core, half 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Far-red light-absorbing allophycocyanin core

EntireName: Far-red light-absorbing allophycocyanin core
Components
  • Complex: Far-red light-absorbing allophycocyanin core
    • Protein or peptide: ApcD5
    • Protein or peptide: ApcB2
    • Protein or peptide: ApcD3
    • Protein or peptide: ApcD2
    • Protein or peptide: ApcF
    • Protein or peptide: ApcE2
    • Protein or peptide: ApcC
  • Ligand: PHYCOCYANOBILIN
  • Ligand: mesobiliverdin IX(alpha)
  • Ligand: CHLORIDE ION

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Supramolecule #1: Far-red light-absorbing allophycocyanin core

SupramoleculeName: Far-red light-absorbing allophycocyanin core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)

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Macromolecule #1: ApcD5

MacromoleculeName: ApcD5 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 17.837252 KDa
SequenceString:
MSLVTELILS ADSEARYPAP KELRIFQDFV KTGEQRVRIA KALAANEERI VQNGSQKFWE RCPNTPSNSG VDRKTASCQR DQGWYVRLI AYSILAGSER PLEDIGTVGI KEMYNNLEIP IRNIAECMRC LKEEAMAVLS DEDAQEVAAY FDLIIQSLS

UniProtKB: Phycobilisome protein

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Macromolecule #2: ApcB2

MacromoleculeName: ApcB2 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 17.501822 KDa
SequenceString:
MQDAITTLIN TSDAQGKYLD DSSLDTLQEY FRSGDLRAKA AMTISANAST IVTKTVAKSL LYTDITGPGG (MEN)MYTCR RYA ACIRDMDFFL RYGTYAMLAG DASILDERVL NGLKETYNSL GVPVGATIRA VQAMKEVVND MLGAEAGKEV GYYFDHI CS GLS

UniProtKB: Allophycocyanin, beta subunit

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Macromolecule #3: ApcD3

MacromoleculeName: ApcD3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 20.339404 KDa
SequenceString:
MSIVKQIISN ADEELRYPTP GELEMIRSFC KTGASQIQLA KTLESHAPTI VERGTRKFWQ ICPRTPSNSG SPRKTEAAQR DMSWYIRLI SYCLLAGNDQ PLREIGLLGM KELYTNIGIP LDNILQYLRC LKAEAIALLS EAEAEAIIPY FDQIIQELVR P GPSYFGIK DRSARQSARQ AAA

UniProtKB: Phycobilisome protein

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Macromolecule #4: ApcD2

MacromoleculeName: ApcD2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 17.891504 KDa
SequenceString:
MSVISQVIAT ADREVRYLSK GELDAINRFF NNGPQRLRIV SILNSNAEEI VEKGARRFWQ RCPITPSNSD NQQFQASCLR DQAWFIRLI SYAVAVGDVD PLEASGVRGV REMYLSLEVP LRSVALCMRS LKEVTLAMLS REDAAEVGPY FDYLIAGLMP

UniProtKB: Phycobilisome protein

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Macromolecule #5: ApcF

MacromoleculeName: ApcF / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 18.950438 KDa
SequenceString:
MRDTVTSLIS NYDTTGRYLD RDAIDSLQSY FITGANRVKV AAMISANAAE ISREAGKKLF EVVPELIRPG G(MEN)AYTT RRY AACLRDMDYY LRYSSYALVA GNNDVLMERV LQGLRETYNS LGVPIAPTVQ GIQIMKEMVK ERASDMGVDD TSFIDQP FD FISREVSEIS V

UniProtKB: Allophycocyanin, beta subunit

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Macromolecule #6: ApcE2

MacromoleculeName: ApcE2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 87.252891 KDa
SequenceString: MTDRTNGGSP VVHPQQYHTV PTAVINGAHQ RDRYPNHSEM QTLSTFLRTG LQRLEIAQTL AQHANEIVAA GGKRIFVGGN PMAYFEQPE ELVGMPGSGY FVAEDYLSPK SRRQTGNGHS VQNSSSSITN PVAWLKGLFF SGKPSVPSRF QAINIADYGA V RMKRSMRD ...String:
MTDRTNGGSP VVHPQQYHTV PTAVINGAHQ RDRYPNHSEM QTLSTFLRTG LQRLEIAQTL AQHANEIVAA GGKRIFVGGN PMAYFEQPE ELVGMPGSGY FVAEDYLSPK SRRQTGNGHS VQNSSSSITN PVAWLKGLFF SGKPSVPSRF QAINIADYGA V RMKRSMRD LGWFLRYITY AVVAGDTSII TVNTRGLRGI IPEDVTVATT VALQEMQWKS LSFFPVDSAA AALVRRYFDV LI ADYQVEK PSDRYRTGVS KHDQGLSFPE SYEDSGCAIP RWVMKPTLPD SEKDAVIRAA YRQVFERDIS GLGTAELTQP ISQ LKGEDG SMELFIRQLG KSRLYRQLFY EPYMISRSIE LACRHFLGRG LSCMEEFQRY FELVADQGFS ALVDALVSSQ EYAD YFGAE TVPYIRGLGI EAQACRNWGP QLDLFKYSAP ARKVPQFVTA FASYRQPLPN QHPYGMGNDP LETQFGAIFP HETTN PAAQ PVHFSEDSRR ILVGHAHRKS HAEISQQIFS LKTLAHKPTK ASESLSFFPS SDSRQHSVES VILAAYRQVF GCEVLG SQR HQAAETQLKG GLITVREFVR QLAKSRSFRQ AYWENLYMTK AAEIIHRRLL GRPTYGRRET SKYYDICGRQ GFYALVD AL IDSDDYRTAF GENTVPYERY VTPRGLALRS PKGPVAISKL RDNPHTVGEY MMRYQPPAAN ISPRSPLNNS ASNRQPAT A RHSDNGALED RSASSTEPAT SKSSVALADP PASDEPAASE DSAISENIEP SMAVALQETS SD

UniProtKB: Phycobiliprotein ApcE

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Macromolecule #7: ApcC

MacromoleculeName: ApcC / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 7.80407 KDa
SequenceString:
MRMFRVTACV PSQTRIRTQR ELQNTYFTKL VPYDNWFKEQ QRIQKMGGTI VKVELATGRR GANTGLA

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: 16 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Macromolecule #9: mesobiliverdin IX(alpha)

MacromoleculeName: mesobiliverdin IX(alpha) / type: ligand / ID: 9 / Number of copies: 2 / Formula: M1V
Molecular weightTheoretical: 586.678 Da
Chemical component information

ChemComp-M1V:
mesobiliverdin IX(alpha)

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Macromolecule #10: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: homology, see publication
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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