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Open data
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Basic information
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Title | PSI-AcpPCI supercomplex from Symbiodinium | |||||||||||||||||||||||||||
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![]() | Photosysrem I / Photosynthesis / Dinoflagellate | |||||||||||||||||||||||||||
Function / homology | Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / photosystem I / photosynthesis / membrane / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein![]() | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||||||||||||||||||||
![]() | Li ZH / Li XY / Wang WD | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||||||||||||||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 257.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 46.3 KB 46.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.8 KB | Display | ![]() |
Images | ![]() | 97 KB | ||
Filedesc metadata | ![]() | 10.1 KB | ||
Others | ![]() ![]() | 475.8 MB 475.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jzeMC ![]() 8jw0C ![]() 8jzfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : PSI-AcpPCI supercomplex from Symbiodinium
+Supramolecule #1: PSI-AcpPCI supercomplex from Symbiodinium
+Macromolecule #1: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7
+Macromolecule #2: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6
+Macromolecule #3: Photosystem I unk
+Macromolecule #4: Photosystem I unk
+Macromolecule #5: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8
+Macromolecule #6: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10
+Macromolecule #7: Photosystem I PsaC
+Macromolecule #8: Photosystem I PsaD
+Macromolecule #9: Photosystem I PsaE
+Macromolecule #10: Photosystem I PsaF
+Macromolecule #11: Photosystem I PsaR
+Macromolecule #12: Photosystem I PsaI
+Macromolecule #13: Photosystem I PsaJ
+Macromolecule #14: Photosystem I PsaL
+Macromolecule #15: Photosystem I PsaM
+Macromolecule #16: Photosystem I PsaA
+Macromolecule #17: Photosystem I PsaB
+Macromolecule #18: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11
+Macromolecule #19: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9
+Macromolecule #20: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2
+Macromolecule #21: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12
+Macromolecule #22: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3
+Macromolecule #23: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5
+Macromolecule #24: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4
+Macromolecule #25: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13
+Macromolecule #26: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15
+Macromolecule #27: Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14
+Macromolecule #28: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
+Macromolecule #29: [(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9...
+Macromolecule #30: CHLOROPHYLL A
+Macromolecule #31: Chlorophyll c1
+Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #34: PERIDININ
+Macromolecule #35: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #36: IRON/SULFUR CLUSTER
+Macromolecule #37: BETA-CAROTENE
+Macromolecule #38: PHYLLOQUINONE
+Macromolecule #39: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |