+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34930 | ||||||||||||||||||||||||||||||
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Title | Bry-LHCII heterotrimer of Bryopsis corticulans | ||||||||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||||||||
Sample |
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Keywords | Light-harvesting complexes / siphonaxanthin / siphonein / PHOTOSYNTHESIS | ||||||||||||||||||||||||||||||
Biological species | Bryopsis corticulans (plant) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | ||||||||||||||||||||||||||||||
Authors | Li ZH / Shen JR / Wang WD | ||||||||||||||||||||||||||||||
Funding support | China, 9 items
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Citation | Journal: Structure / Year: 2023 Title: Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans. Authors: Zhenhua Li / Cuicui Zhou / Songhao Zhao / Jinyang Zhang / Xueyang Liu / Min Sang / Xiaochun Qin / Yanyan Yang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Wenda Wang / Abstract: Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the ...Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34930.map.gz | 32 MB | EMDB map data format | |
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Header (meta data) | emd-34930-v30.xml emd-34930.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34930_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_34930.png | 102.7 KB | ||
Filedesc metadata | emd-34930.cif.gz | 5.9 KB | ||
Others | emd_34930_half_map_1.map.gz emd_34930_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34930 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34930 | HTTPS FTP |
-Validation report
Summary document | emd_34930_validation.pdf.gz | 702.9 KB | Display | EMDB validaton report |
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Full document | emd_34930_full_validation.pdf.gz | 702.5 KB | Display | |
Data in XML | emd_34930_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_34930_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34930 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34930 | HTTPS FTP |
-Related structure data
Related structure data | 8hpdMC 8hlvC 8hq8C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34930.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_34930_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34930_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Bryopsis corticulans chlorophyll a/b-type light-harvesting comple...
+Supramolecule #1: Bryopsis corticulans chlorophyll a/b-type light-harvesting comple...
+Macromolecule #1: siphonaxanthin chlorophyll a/b binding light-harvesting complex I...
+Macromolecule #2: siphonaxanthin chlorophyll a/b binding light-harvesting complex I...
+Macromolecule #3: siphonaxanthin chlorophyll a/b binding light-harvesting complex I...
+Macromolecule #4: Siphonein
+Macromolecule #5: Siphonaxanthin
+Macromolecule #6: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #7: CHLOROPHYLL B
+Macromolecule #8: CHLOROPHYLL A
+Macromolecule #9: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |