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- EMDB-42281: Structure of the far-red light-absorbing allophycocyanin core exp... -

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Basic information

Entry
Database: EMDB / ID: EMD-42281
TitleStructure of the far-red light-absorbing allophycocyanin core expressed during FaRLiP
Map datasharpened and masked
Sample
  • Complex: Far-red light-absorbing allophycocyanin core
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit
    • Protein or peptide: Ribulose bisphosphate carboxylase large subunit
  • Ligand: RIBULOSE-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordslight-harvesting / allophycocyanin / phycocyanobilin / PHOTOSYNTHESIS
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain ...Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 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_42281.png

Downloads & links

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Map

FileDownload / File: emd_42281.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened and masked
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.10184023 - 0.16187456
Average (Standard dev.)0.00046650332 (±0.0076316423)
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: sharpened and unmasked

Fileemd_42281_additional_1.map
Annotationsharpened and unmasked
Projections & Slices
AxesZYX

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Additional map: unsharpened

Fileemd_42281_additional_2.map
Annotationunsharpened
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Half map: half 1

Fileemd_42281_half_map_1.map
Annotationhalf 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_42281_half_map_2.map
Annotationhalf 2
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Histogram

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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: Ribulose bisphosphate carboxylase small subunit
    • Protein or peptide: Ribulose bisphosphate carboxylase large subunit
  • Ligand: RIBULOSE-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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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-#2
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)

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Macromolecule #1: Ribulose bisphosphate carboxylase small subunit

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 13.517304 KDa
SequenceString:
MKTLPKERRY ETLSYLPPLT DQQIEKQINY CLQMGYIPAV EFNETSEPEA YYWTMWKLPL FGANNTRAVL DEIQACRSEY GNCFIRVVG FDNVKQCQAV SFIVHKPGSN NSSGYRY

UniProtKB: Ribulose bisphosphate carboxylase small subunit

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Macromolecule #2: Ribulose bisphosphate carboxylase large subunit

MacromoleculeName: Ribulose bisphosphate carboxylase large subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Molecular weightTheoretical: 53.031836 KDa
SequenceString: MSYSQTQSKS GAGYDAGVQD YRLTYYAPDY TPRDTDILAA FRMTPQPGVP PEECAAAVAA ESSTGTWTTV WTDLLTDMDR YRGRCYDIE PVPGEDNQYI AYVAYPLDLF EEGSVTNLLT SLVGNVFGFK ALRALRLEDL RIPVAYVKTF QGPPHGIQVE R DRINKYGR ...String:
MSYSQTQSKS GAGYDAGVQD YRLTYYAPDY TPRDTDILAA FRMTPQPGVP PEECAAAVAA ESSTGTWTTV WTDLLTDMDR YRGRCYDIE PVPGEDNQYI AYVAYPLDLF EEGSVTNLLT SLVGNVFGFK ALRALRLEDL RIPVAYVKTF QGPPHGIQVE R DRINKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFT(KCX)DDENIN SQPFQRWRDR FLFVADAIHK SQAETGEI K GHYLNVTAAT CEEMMKRAAY AKELEMPIVM HDFLTGGFTA NTTLAHWCRD NGILLHIHRA MHAVIDRQKN HGIHFRVLA KCLRMSGGDH IHTGTVVGKL EGDRAGTLGF VDLLRENYIE QDKSRGVYFT QDWASMPGVM AVASGGIHVW HMPALVEIFG DDSVLQFGG GTLGHPWGNA PGATANRVAL EACVQARNEG RNLAREGGDI IREACKWSPE LAAACELWKE IKFEFDTVDT I

UniProtKB: Ribulose bisphosphate carboxylase large chain

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Macromolecule #3: RIBULOSE-1,5-DIPHOSPHATE

MacromoleculeName: RIBULOSE-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: RUB
Molecular weightTheoretical: 310.09 Da
Chemical component information

ChemComp-RUB:
RIBULOSE-1,5-DIPHOSPHATE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 904 / 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

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: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57918
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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