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- EMDB-35766: Structure and characteristics of a photosystem II supercomplex co... -
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Basic information
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Title | Structure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana | ||||||||||||||||||||||||||||||
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![]() | PSII supercomplex / LHCX / FCP / PHOTOSYNTHESIS | ||||||||||||||||||||||||||||||
Function / homology | ![]() light-harvesting complex / cytochrome c-heme linkage / photosystem II assembly / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II stabilization / photosystem II / photosystem II reaction center / thylakoid / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...light-harvesting complex / cytochrome c-heme linkage / photosystem II assembly / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II stabilization / photosystem II / photosystem II reaction center / thylakoid / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / plastid / extrinsic component of membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / response to light stimulus / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / chloroplast / electron transfer activity / protein stabilization / iron ion binding / heme binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | ||||||||||||||||||||||||||||||
![]() | Feng Y / Li ZH / Wang WD / Shen JR | ||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII. Authors: Yue Feng / Zhenhua Li / Xiaoyi Li / Lili Shen / Xueyang Liu / Cuicui Zhou / Jinyang Zhang / Min Sang / Guangye Han / Wenqiang Yang / Tingyun Kuang / Wenda Wang / Jian-Ren Shen / ![]() ![]() Abstract: Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We ...Diatoms rely on fucoxanthin chlorophyll -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 239.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 51 KB 51 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.5 KB | Display | ![]() |
Images | ![]() | 123.5 KB | ||
Filedesc metadata | ![]() | 10.9 KB | ||
Others | ![]() ![]() | 442.4 MB 442.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iwhMC ![]() 8j0dC 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: 0.88 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35766_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35766_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Structure of PSII-FCPII supercomplex containing monomeric LHCX an...
+Supramolecule #1: Structure of PSII-FCPII supercomplex containing monomeric LHCX an...
+Macromolecule #1: Photosystem II protein D1
+Macromolecule #2: Photosystem II CP47 reaction center protein
+Macromolecule #3: Photosystem II CP43 reaction center protein
+Macromolecule #4: Photosystem II D2 protein
+Macromolecule #5: Cytochrome b559 subunit alpha
+Macromolecule #6: Cytochrome b559 subunit beta
+Macromolecule #7: Photosystem II Psb31 protein domain-containing protein
+Macromolecule #8: Photosystem II reaction center protein H
+Macromolecule #9: Photosystem II reaction center protein I
+Macromolecule #10: Photosystem II reaction center protein J
+Macromolecule #11: Photosystem II reaction center protein K
+Macromolecule #12: Photosystem II reaction center protein L
+Macromolecule #13: Photosystem II reaction center M protein, plastid
+Macromolecule #14: Photosystem II subunit, PsbN.
+Macromolecule #15: Oxygen-evolving enhancer protein 1
+Macromolecule #16: Photosystem II reaction center protein T
+Macromolecule #17: PS II complex 12 kDa extrinsic protein
+Macromolecule #18: Cytochrome c-550
+Macromolecule #19: Photosystem II subunit, PsbW
+Macromolecule #20: Photosystem II reaction center X protein
+Macromolecule #21: Photosystem II reaction center protein Z
+Macromolecule #22: Fucoxanthin chl a/c protein, lhca clade
+Macromolecule #23: Fucoxanthin-chlorophyll a-c binding protein, plastid
+Macromolecule #24: Fucoxanthin chlorophyll a/c protein 6
+Macromolecule #25: Fucoxanthin chlorophyll a/c protein 5
+Macromolecule #26: Fucoxanthin chlorophyll a/c protein-LI818 clade
+Macromolecule #27: Photosystem II reaction center protein Ycf12
+Macromolecule #28: Photosystem II subunit, PsbQ.
+Macromolecule #29: Fucoxanthin chlorophyll a/c light-harvesting protein, major type
+Macromolecule #30: BETA-CAROTENE
+Macromolecule #31: CA-MN4-O5 CLUSTER
+Macromolecule #32: CHLORIDE ION
+Macromolecule #33: CHLOROPHYLL A
+Macromolecule #34: PHEOPHYTIN A
+Macromolecule #35: BICARBONATE ION
+Macromolecule #36: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #37: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #38: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #39: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #40: FE (II) ION
+Macromolecule #41: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #42: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #43: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #44: Chlorophyll c1
+Macromolecule #45: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
+Macromolecule #46: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
+Macromolecule #47: Chlorophyll c2
+Macromolecule #48: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...
-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: 6.5 |
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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 |