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- PDB-3jbb: Characterization of red-shifted phycobiliprotein complexes isolat... -

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Entry
Database: PDB / ID: 3jbb
TitleCharacterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris
Components
  • allophycocyanin beta chain
  • allophycocyanin subunit alpha-B
KeywordsPHOTOSYNTHESIS / alpha-helical phycobiliprotein / light harvesting / phycocyano methylation on ASN71 in APCB SUBUNIT / phycobilisome
Function / homology
Function and homology information


: / : / phycobilisome / photosynthesis
Similarity search - Function
Allophycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Allophycocyanin subunit alpha-B / Allophycocyanin beta chain
Similarity search - Component
Biological speciesHalomicronema hongdechloris (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 26 Å
AuthorsLi, Y. / Lin, Y. / Garvey, C. / Birch, D. / Corkery, R.W. / Loughlin, P.C. / Scheer, H. / Willows, R.D. / Chen, M.
Citation
Journal: Biochim Biophys Acta / Year: 2016
Title: Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris.
Authors: Yaqiong Li / Yuankui Lin / Christopher J Garvey / Debra Birch / Robert W Corkery / Patrick C Loughlin / Hugo Scheer / Robert D Willows / Min Chen /
Abstract: Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria and some algae. It is commonly accepted that these complexes only absorb green and orange light, complementing ...Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria and some algae. It is commonly accepted that these complexes only absorb green and orange light, complementing chlorophyll absorbance. Here, we present a new phycobilisome derived complex that consists only of allophycocyanin core subunits, having red-shifted absorption peaks of 653 and 712 nm. These red-shifted phycobiliprotein complexes were isolated from the chlorophyll f-containing cyanobacterium, Halomicronema hongdechloris, grown under monochromatic 730 nm-wavelength (far-red) light. The 3D model obtained from single particle analysis reveals a double disk assembly of 120-145 Å with two α/β allophycocyanin trimers fitting into the two separated disks. They are significantly smaller than typical phycobilisomes formed from allophycocyanin subunits and core-membrane linker proteins, which fit well with a reduced distance between thylakoid membranes observed from cells grown under far-red light. Spectral analysis of the dissociated and denatured phycobiliprotein complexes grown under both these light conditions shows that the same bilin chromophore, phycocyanobilin, is exclusively used. Our findings show that red-shifted phycobilisomes are required for assisting efficient far-red light harvesting. Their discovery provides new insights into the molecular mechanisms of light harvesting under extreme conditions for photosynthesis, as well as the strategies involved in flexible chromatic acclimation to diverse light conditions.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2014
Title: The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes.
Authors: Pan Pan Peng / Liang Liang Dong / Ya Fang Sun / Xiao Li Zeng / Wen Long Ding / Hugo Scheer / Xiaojing Yang / Kai Hong Zhao /
Abstract: Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the ...Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB)3] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10(6) Å(3). While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λmax = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Assembly

Deposited unit
A: allophycocyanin subunit alpha-B
B: allophycocyanin beta chain
C: allophycocyanin subunit alpha-B
D: allophycocyanin beta chain
E: allophycocyanin subunit alpha-B
F: allophycocyanin beta chain
G: allophycocyanin subunit alpha-B
H: allophycocyanin beta chain
I: allophycocyanin subunit alpha-B
J: allophycocyanin beta chain
K: allophycocyanin subunit alpha-B
L: allophycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,18866
Polymers216,08912
Non-polymers11,09954
Water43,1642396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
allophycocyanin subunit alpha-B /


Mass: 18769.273 Da / Num. of mol.: 6 / Fragment: APCD subunit (SEE REMARK 999) / Source method: isolated from a natural source / Source: (natural) Halomicronema hongdechloris (bacteria) / References: UniProt: A0A0R4I959*PLUS
#2: Protein
allophycocyanin beta chain


Mass: 17245.629 Da / Num. of mol.: 6 / Fragment: APCB subunit (SEE REMARK 999) / Source method: isolated from a natural source / Source: (natural) Halomicronema hongdechloris (bacteria) / References: UniProt: A0A0R4I960*PLUS
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2396 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE IMAGED PROTEINS ARE FROM HALOMICRONEMA HONGDECHLORIS, BUT THE MODELED SEQUENCES ARE FROM ...THE IMAGED PROTEINS ARE FROM HALOMICRONEMA HONGDECHLORIS, BUT THE MODELED SEQUENCES ARE FROM SYNECHOCYSTIS PCC 6803.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY / Number of used crystals: 1
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1Red-shifted phycobilisomes from Halomicronema hongdechlorisCOMPLEXTwo APC trimers linked with APC E0
2APC phycobilisome complex1
Buffer solutionName: 0.8 M phosphate buffer / pH: 7.5 / Details: 0.8 M phosphate buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO / Details: 2% uranyl acetate for 2-3 seconds
EM stainingType: NEGATIVE / Material: uranyl acetate
Specimen supportDetails: 200 mesh gold grid with thin carbon support

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM10 / Date: Jun 8, 2015 / Details: PHILIPS CM10
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 180000 X / Nominal defocus max: 3000 nm
Specimen holderSpecimen holder model: PHILIPS ROTATION HOLDER
Image recordingFilm or detector model: GENERIC IMAGE PLATES
Image scansNum. digital images: 12

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EMAN23D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionMethod: Cross-common lines / Resolution: 26 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 420 / Nominal pixel size: 3.8 Å / Actual pixel size: 3.8 Å
Details: (Single particle details: Semiautomatic selection using e2boxer.py swarm function) (Single particle--Applied symmetry: D3)
Num. of class averages: 32 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: REFINEMENT PROTOCOL--rigid body DETAILS--Two trimers were fitted to each end of the EM map. 99.5% of atoms fit within the map at contour level 0.87
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
14PO5

4po5

A1
24PO5

4po5

B1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms14880 0 726 2396 18002

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