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- PDB-8jze: PSI-AcpPCI supercomplex from Symbiodinium -

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Entry
Database: PDB / ID: 8jze
TitlePSI-AcpPCI supercomplex from Symbiodinium
Components
  • (Chlorophyll a-chlorophyll c-peridinin-protein-complex I- ...) x 14
  • (Photosystem I ...) x 13
KeywordsPHOTOSYNTHESIS / Photosysrem I / Dinoflagellate
Function / homology
Function and homology information


photosystem I / photosynthesis / membrane
Similarity search - Function
Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PERIDININ / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL A / Chem-DD6 / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PERIDININ / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / : / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesSymbiodinium (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsLi, Z.H. / Li, X.Y. / Wang, W.D.
Funding support China, 8items
OrganizationGrant numberCountry
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates.
Authors: Xiaoyi Li / Zhenhua Li / Fangfang Wang / Songhao Zhao / Caizhe Xu / Zhiyuan Mao / Jialin Duan / Yue Feng / Yang Yang / Lili Shen / Guanglei Wang / Yanyan Yang / Long-Jiang Yu / Min Sang / ...Authors: Xiaoyi Li / Zhenhua Li / Fangfang Wang / Songhao Zhao / Caizhe Xu / Zhiyuan Mao / Jialin Duan / Yue Feng / Yang Yang / Lili Shen / Guanglei Wang / Yanyan Yang / Long-Jiang Yu / Min Sang / Guangye Han / Xuchu Wang / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the ...Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) /-peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls and and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7
K: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6
z: Photosystem I unk
y: Photosystem I unk
G: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8
A: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10
c: Photosystem I PsaC
d: Photosystem I PsaD
e: Photosystem I PsaE
f: Photosystem I PsaF
h: Photosystem I PsaR
i: Photosystem I PsaI
j: Photosystem I PsaJ
l: Photosystem I PsaL
m: Photosystem I PsaM
a: Photosystem I PsaA
b: Photosystem I PsaB
B: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11
D: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9
F: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2
H: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12
J: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3
L: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5
M: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4
N: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13
O: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15
P: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)851,244369
Polymers583,61027
Non-polymers267,634342
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chlorophyll a-chlorophyll c-peridinin-protein-complex I- ... , 14 types, 14 molecules IKGABDFHJLMNOP

#1: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7


Mass: 21839.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#2: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6


Mass: 19596.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#5: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8


Mass: 24560.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#6: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10


Mass: 20093.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#18: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11


Mass: 21264.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#19: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9


Mass: 17493.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#20: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2


Mass: 19335.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#21: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12


Mass: 17109.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#22: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3


Mass: 22912.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#23: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5


Mass: 20585.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#24: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4


Mass: 19381.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#25: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13


Mass: 17119.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#26: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15


Mass: 17422.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#27: Protein Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14


Mass: 17355.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)

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Photosystem I ... , 13 types, 13 molecules zycdefhijlmab

#3: Protein Photosystem I unk /


Mass: 6656.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#4: Protein Photosystem I unk /


Mass: 11166.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#7: Protein Photosystem I PsaC /


Mass: 9425.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#8: Protein Photosystem I PsaD /


Mass: 24878.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#9: Protein Photosystem I PsaE /


Mass: 8266.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#10: Protein Photosystem I PsaF /


Mass: 20609.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#11: Protein Photosystem I PsaR /


Mass: 15221.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote) / References: UniProt: A0A812Q823
#12: Protein Photosystem I PsaI /


Mass: 13699.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote) / References: UniProt: A0A812IJ75
#13: Protein Photosystem I PsaJ /


Mass: 11153.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote) / References: UniProt: A0A812LLR4
#14: Protein Photosystem I PsaL /


Mass: 27708.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#15: Protein Photosystem I PsaM /


Mass: 8527.976 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote) / References: UniProt: A0A812M556
#16: Protein Photosystem I PsaA /


Mass: 75785.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)
#17: Protein Photosystem I PsaB /


Mass: 74438.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Symbiodinium (eukaryote)

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Sugars , 1 types, 7 molecules

#32: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 11 types, 335 molecules

#28: Chemical...
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C40H54O3 / Feature type: SUBJECT OF INVESTIGATION
#29: Chemical
ChemComp-UIX / [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate / Dinoxanthin


Mass: 642.907 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C42H58O5 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 201 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#31: Chemical...
ChemComp-KC1 / Chlorophyll c1 / Chlorophyll c


Mass: 610.941 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C35H30MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#34: Chemical...
ChemComp-PID / PERIDININ / Peridinin


Mass: 630.810 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C39H50O7 / Feature type: SUBJECT OF INVESTIGATION
#35: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S / Feature type: SUBJECT OF INVESTIGATION
#36: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#37: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H56
#38: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#39: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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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: PSI-AcpPCI supercomplex from Symbiodinium / Type: COMPLEX / Entity ID: #1-#27 / Source: NATURAL
Source (natural)Organism: Symbiodinium (eukaryote)
Buffer solutionpH: 7.5
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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46321 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00558907
ELECTRON MICROSCOPYf_angle_d1.09784183
ELECTRON MICROSCOPYf_dihedral_angle_d18.41618703
ELECTRON MICROSCOPYf_chiral_restr0.0497527
ELECTRON MICROSCOPYf_plane_restr0.00510963

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