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- PDB-8uhe: Structure of the far-red light-absorbing allophycocyanin core exp... -

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Basic information

Entry
Database: PDB / ID: 8uhe
TitleStructure of the far-red light-absorbing allophycocyanin core expressed during FaRLiP
Components
  • ApcB2
  • ApcC
  • ApcD2
  • ApcD3
  • ApcD5
  • ApcE2
  • ApcF
KeywordsPHOTOSYNTHESIS / light-harvesting / allophycocyanin / 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
PHYCOCYANOBILIN / mesobiliverdin IX(alpha) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsGisriel, C.J. / Bryant, D.A. / Brudvig, G.W. / Shen, G.
Funding support United States, 3items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ApcD5
B: ApcB2
C: ApcD3
D: ApcB2
E: ApcD5
F: ApcB2
G: ApcD5
H: ApcB2
I: ApcD2
J: ApcF
K: ApcE2
L: ApcB2
M: ApcD5
N: ApcB2
O: ApcD5
P: ApcB2
Q: ApcD5
R: ApcB2
S: ApcC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,90438
Polymers399,27619
Non-polymers10,62819
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 19 molecules AEGMOQBDFHLNPRCIJKS

#1: Protein
ApcD5


Mass: 17837.252 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WKI9
#2: Protein
ApcB2


Mass: 17501.822 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WKI8
#3: Protein ApcD3


Mass: 20339.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WKI4
#4: Protein ApcD2


Mass: 17891.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WKI7
#5: Protein ApcF


Mass: 18950.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WIH2
#6: Protein ApcE2


Mass: 87252.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WKI6
#7: Protein ApcC


Mass: 7804.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechococcus sp. PCC 7335 (bacteria) / References: UniProt: B4WI75

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Non-polymers , 3 types, 19 molecules

#8: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C33H40N4O6
#9: Chemical ChemComp-M1V / mesobiliverdin IX(alpha)


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Far-red light-absorbing allophycocyanin core / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113162 / Symmetry type: POINT

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