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- PDB-8ddy: Helical rods of far-red light-absorbing allophycocyanin in Synech... -

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Basic information

Entry
Database: PDB / ID: 8ddy
TitleHelical rods of far-red light-absorbing allophycocyanin in Synechococcus sp.
Components
  • Allophycocyanin subunit alpha
  • Allophycocyanin subunit beta
KeywordsPHOTOSYNTHESIS / Allophycocyanin / phycobiliprotein / photosystem / energy transfer / cyanobacteria / far-red light / FaRLiP / LoLiP
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Allophycocyanin subunit beta / Allophycocyanin subunit alpha
Similarity search - Component
Biological speciesSynechococcus sp. 63AY4M1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsGisriel, C.J. / Shen, G.S. / Soulier, N.T. / Flesher, D.A. / Brudvig, G.W. / Bryant, D.A.
Funding support United States, 5items
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, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allophycocyanin subunit alpha
B: Allophycocyanin subunit beta
C: Allophycocyanin subunit alpha
D: Allophycocyanin subunit beta
E: Allophycocyanin subunit alpha
F: Allophycocyanin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,35515
Polymers114,7166
Non-polymers3,6399
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "E"
d_2ens_1chain "C"
d_3ens_1chain "A"
d_1ens_2chain "D"
d_2ens_2chain "B"
d_3ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERPHEPHEEE27 - 18427 - 184
d_12ens_1CYCCYCCYCCYCEM201
d_21ens_1SERSERPHEPHECC27 - 18427 - 184
d_22ens_1CYCCYCCYCCYCCJ201
d_31ens_1SERSERPHEPHEAA27 - 18427 - 184
d_32ens_1CYCCYCCYCCYCAG201
d_11ens_2METMETLEULEUDD1 - 1601 - 160
d_12ens_2CYCCYCCYCCYCDK201
d_21ens_2METMETLEULEUBB1 - 1601 - 160
d_22ens_2CYCCYCCYCCYCBH201
d_31ens_2METMETLEULEUFF1 - 1601 - 160
d_32ens_2CYCCYCCYCCYCFN201

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.203266180814, 0.979123513455, -7.16761279866E-5), (-0.979120616455, -0.203265756465, -0.00241881809332), (-0.00238289097231, -0.000421484341294, 0.999997072086)17.6705594243, 135.812816772, 10.5186055414
2given(-0.918749770196, -0.394818197726, -0.00417738068615), (0.394814330994, -0.918759266, 0.00174790753813), (-0.004528112917, -4.3400111928E-5, 0.999989747102)147.011100554, 91.0873506759, 21.0294920698
3given(-0.204125925499, 0.978935861413, -0.00414557349127), (-0.978944300512, -0.2041205022, 0.00169619497228), (0.00081426954337, 0.00440452291018, 0.999989968521)17.8392255653, 135.674689049, 10.1250485548
4given(-0.197611778999, -0.980269464735, 0.00462182958105), (0.980277307196, -0.1975971999, 0.00342747550534), (-0.00244658899538, 0.00520798418811, 0.999983445414)136.030315089, 9.90767661163, -10.3218166517

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Components

#1: Protein Allophycocyanin subunit alpha


Mass: 20526.518 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. 63AY4M1 (bacteria) / Gene: SYN60AY4M2_00015 / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: A0A2G8PAX6
#2: Protein Allophycocyanin subunit beta


Mass: 17712.303 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. 63AY4M1 (bacteria) / Gene: SYN60AY4M2_00020 / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: A0A2G8PA94
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Far-red light allophycocyanin / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Synechococcus sp. 63AY4M1 (bacteria)
Source (recombinant)Organism: Synechococcus sp. PCC 7002 (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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 59.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74095 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01057764
ELECTRON MICROSCOPYf_angle_d1.642710518
ELECTRON MICROSCOPYf_chiral_restr0.0641176
ELECTRON MICROSCOPYf_plane_restr0.00931335
ELECTRON MICROSCOPYf_dihedral_angle_d23.89642907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints0.000711175053831
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000696727699685
ens_2d_2BELECTRON MICROSCOPYNCS constraints0.0051991330527
ens_2d_3FELECTRON MICROSCOPYNCS constraints0.0033362234522

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