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- PDB-9i1r: Structure of the bicylindrical allophycocyanin core expressed dur... -

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Basic information

Entry
Database: PDB / ID: 9i1r
TitleStructure of the bicylindrical allophycocyanin core expressed during far-red light photoacclimation (FaRLiP)
Components
  • (Allophycocyanin ...) x 2
  • (Phycocyanin) x 3
  • Phycobiliprotein ApcE
  • Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
KeywordsPHOTOSYNTHESIS / Phycobilisome / Allophycocyanin / Complex
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 / Phycobiliprotein ApcE / Allophycocyanin beta subunit apoprotein / Phycocyanin / Phycocyanin / Phycocyanin / Allophycocyanin beta-18 subunit apoprotein / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Similarity search - Component
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsConsoli, G. / Leong, H.F. / Davis, G.A. / Richardson, T. / McInnes, A. / Murray, J.W. / Fantuzzi, A. / Rutherford, A.W.
Funding supportEuropean Union, United Kingdom, 6items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission955520European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Royal SocietyRoyal Society Research Professorship 2024 United Kingdom
CitationJournal: Commun Biol / Year: 2025
Title: Structure of a stripped-down and tuned-up far-red phycobilisome.
Authors: Giovanni Consoli / Ho Fong Leong / Geoffry A Davis / Tom Richardson / Aiysha McInnes / James W Murray / Andrea Fantuzzi / A William Rutherford /
Abstract: A diverse subset of cyanobacteria can transiently modify their photosynthetic machinery during far-red light photoacclimation to drive photosynthesis with less energetic photons (700 nm-800 nm). ...A diverse subset of cyanobacteria can transiently modify their photosynthetic machinery during far-red light photoacclimation to drive photosynthesis with less energetic photons (700 nm-800 nm). To achieve this, all the main light-driven components of the photosynthetic apparatus, including their allophycocyanin antenna, are replaced with red-shifted paralogues. Recent studies based on the structure of an incomplete complex provided some insights into the tuning of the far-red phycobiliproteins. Here, we solved the structure of the intact bicylindrical allophycocyanin complex from the cyanobacterium Chroococcidiopsis thermalis PCC 7203 at a resolution of 2.51 Å determined by Cryo-electron microscopy single particle analysis. A comparison between conserved structural features in far-red and white light allophycocyanin cores provides insight on the evolutionary adaptations needed to optimize excitation energy transfer in the far-red light adapted photosynthetic apparatus. The reduction in antenna size in far-red photosynthesis suggests a need to optimize membrane packing to increase the number of photosystems and tune the ratio between chlorophyll f molecules and bilin pigments, while the wider spread in the absorption range of the bilins suggests faster and more efficient excitation energy transfer to far-red Photosystem II by limiting backflow of excitation from the reaction centres to the far-red bilin pigments.
History
DepositionJan 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycocyanin
B: Allophycocyanin beta subunit apoprotein
C: Phycocyanin
D: Allophycocyanin beta subunit apoprotein
E: Phycocyanin
F: Allophycocyanin beta subunit apoprotein
G: Phycocyanin
H: Allophycocyanin beta subunit apoprotein
I: Phycocyanin
J: Allophycocyanin beta-18 subunit apoprotein
K: Phycobiliprotein ApcE
L: Allophycocyanin beta subunit apoprotein
M: Phycocyanin
N: Allophycocyanin beta subunit apoprotein
O: Phycocyanin
P: Allophycocyanin beta subunit apoprotein
Q: Phycocyanin
R: Allophycocyanin beta subunit apoprotein
S: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
T: Phycocyanin
U: Allophycocyanin beta subunit apoprotein
V: Phycocyanin
W: Allophycocyanin beta subunit apoprotein
X: Phycocyanin
Y: Allophycocyanin beta subunit apoprotein
a: Phycocyanin
b: Allophycocyanin beta subunit apoprotein
c: Phycocyanin
d: Allophycocyanin beta subunit apoprotein
e: Phycocyanin
f: Allophycocyanin beta subunit apoprotein
g: Phycocyanin
h: Allophycocyanin beta subunit apoprotein
i: Phycocyanin
j: Allophycocyanin beta-18 subunit apoprotein
k: Phycobiliprotein ApcE
l: Allophycocyanin beta subunit apoprotein
m: Phycocyanin
n: Allophycocyanin beta subunit apoprotein
o: Phycocyanin
p: Allophycocyanin beta subunit apoprotein
q: Phycocyanin
r: Allophycocyanin beta subunit apoprotein
s: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
t: Phycocyanin
u: Allophycocyanin beta subunit apoprotein
v: Phycocyanin
w: Allophycocyanin beta subunit apoprotein
x: Phycocyanin
y: Allophycocyanin beta subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,045,22098
Polymers1,016,96250
Non-polymers28,25748
Water36020
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 , 5 types, 26 molecules AEGMOQTVXaegmoqtvxCcIiKkSs

#1: Protein
Phycocyanin


Mass: 18117.572 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1032
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TX42
#3: Protein Phycocyanin


Mass: 19978.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1036
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TVZ1
#4: Protein Phycocyanin


Mass: 18260.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1034
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TWK3
#6: Protein Phycobiliprotein ApcE


Mass: 88103.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1035
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TUP3
#7: Protein Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7848.333 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_4322
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9U510

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Allophycocyanin ... , 2 types, 24 molecules BDFHLNPRUWYbdfhlnpruwyJj

#2: Protein ...
Allophycocyanin beta subunit apoprotein


Mass: 17495.893 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1033
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TVG8
#5: Protein Allophycocyanin beta-18 subunit apoprotein


Mass: 18777.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1766
Production host: Chroococcidiopsis thermalis PCC 7203 (bacteria)
References: UniProt: K9TY40

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Non-polymers , 2 types, 68 molecules

#8: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: Bicylindrical far-red light adapted allophycocyanin complex
Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chroococcidiopsis thermalis (bacteria)
Buffer solutionpH: 6.5
Buffer component
IDConc.NameBuffer-ID
120 mMMeS1
25 mMMgCl21
35 mMCaCl21
41.2 MBetaine1
50.03 weight/volumeBeta-DM1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: the sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9397
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
7UCSF ChimeraX1.7model fitting
9PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36300 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 8UHE

8uhe


Accession code: 8UHE / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00572582
ELECTRON MICROSCOPYf_angle_d0.5998388
ELECTRON MICROSCOPYf_dihedral_angle_d7.0612064
ELECTRON MICROSCOPYf_chiral_restr0.03910844
ELECTRON MICROSCOPYf_plane_restr0.00412658

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