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- EMDB-27382: Helical rods of far-red light-absorbing allophycocyanin in Synech... -

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Basic information

Entry
Database: EMDB / ID: EMD-27382
TitleHelical rods of far-red light-absorbing allophycocyanin in Synechococcus sp.
Map dataSharpened and masked far-red light allophycocyanin
Sample
  • Complex: Far-red light allophycocyanin
    • Protein or peptide: Allophycocyanin subunit alpha
    • Protein or peptide: Allophycocyanin subunit beta
  • Ligand: PHYCOCYANOBILIN
  • Ligand: CHLORIDE ION
  • Ligand: water
Function / homologyPhycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / Globin-like superfamily / Allophycocyanin subunit beta / Allophycocyanin subunit alpha
Function and homology information
Biological speciesSynechococcus sp. 63AY4M1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsGisriel CJ / Shen GS / Soulier NT / Flesher DA / Brudvig GW / Bryant DA
Funding support United States, 5 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
Department of Energy (DOE, United States)DE-SC0001423 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008283 United States
CitationJournal: Sci Adv / Year: 2023
Title: Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium.
Authors: Christopher J Gisriel / Eduard Elias / Gaozhong Shen / Nathan T Soulier / David A Flesher / M R Gunner / Gary W Brudvig / Roberta Croce / Donald A Bryant /
Abstract: To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using ...To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo-electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a-containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency.
History
DepositionJun 19, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27382.png

Downloads & links

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Map

FileDownload / File: emd_27382.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened and masked far-red light allophycocyanin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 264 pix.
= 219.648 Å		0.83 Å/pix.
x 264 pix.
= 219.648 Å		0.83 Å/pix.
x 264 pix.
= 219.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.069185816 - 0.13853997
Average (Standard dev.)0.0002648798 (±0.0039718198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 219.64801 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened

Fileemd_27382_additional_1.map
AnnotationUnsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half1

Fileemd_27382_half_map_1.map
AnnotationHalf1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2

Fileemd_27382_half_map_2.map
AnnotationHalf2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Far-red light allophycocyanin

EntireName: Far-red light allophycocyanin
Components
  • Complex: Far-red light allophycocyanin
    • Protein or peptide: Allophycocyanin subunit alpha
    • Protein or peptide: Allophycocyanin subunit beta
  • Ligand: PHYCOCYANOBILIN
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: Far-red light allophycocyanin

SupramoleculeName: Far-red light allophycocyanin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Synechococcus sp. 63AY4M1 (bacteria)

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Macromolecule #1: Allophycocyanin subunit alpha

MacromoleculeName: Allophycocyanin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. 63AY4M1 (bacteria)
Molecular weightTheoretical: 20.526518 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MGHHHHHHHH HHSSGHIEGR HMQAAASMSI VAQVIAQSDA ADRFLSSAEI AKLEDFFSKG QVRIRAAQKL AENEQKIVQE GSKRFWAKC PNTPSNKGNP QKTALCQRDQ GWYIRLVSYC ILAGNDKPLE DIGLNGMREM YISLGVPLPN LRVAMSCLKE V AAGILSSE EMALAAPYFD RLIRAF

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Macromolecule #2: Allophycocyanin subunit beta

MacromoleculeName: Allophycocyanin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. 63AY4M1 (bacteria)
Molecular weightTheoretical: 17.712303 KDa
Recombinant expressionOrganism: Synechococcus sp. PCC 7002 (bacteria)
SequenceString:
MKDTITSLIN PADEKGSYLD AAALEQLNRY FQSGNMRVKA AKTISSSASS IISKTVAKSL LYGDITLPGG (MEN)MYPTR RYA ACLRDLTYFL RYATYAMLAA DPSILDERVL QGLKETYITL GVPIDRVIQA LNAMKEVLTE SLDTEASQEM AVYLDHI IA GLS

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Macromolecule #3: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 3 / Number of copies: 6 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 330 / 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 statefilament

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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: 59.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: PDB ENTRY
PDB model - PDB ID:

4po5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74095
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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