+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36054 | |||||||||
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Title | Structure of FCP trimer in Cyclotella meneghiniana | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cm-FCP-trimer / PHOTOSYNTHESIS | |||||||||
Biological species | Stephanocyclus meneghinianus (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.72 Å | |||||||||
Authors | Shen LL / Li ZH / Shen JR / Wang WD | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana. Authors: Songhao Zhao / Lili Shen / Xiaoyi Li / Qiushuang Tao / Zhenhua Li / Caizhe Xu / Cuicui Zhou / Yanyan Yang / Min Sang / Guangye Han / Long-Jiang Yu / Tingyun Kuang / Jian-Ren Shen / Wenda Wang / Abstract: Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific ...Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36054.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-36054-v30.xml emd-36054.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36054_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_36054.png | 39.6 KB | ||
Filedesc metadata | emd-36054.cif.gz | 5.3 KB | ||
Others | emd_36054_half_map_1.map.gz emd_36054_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36054 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36054 | HTTPS FTP |
-Validation report
Summary document | emd_36054_validation.pdf.gz | 727.4 KB | Display | EMDB validaton report |
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Full document | emd_36054_full_validation.pdf.gz | 727 KB | Display | |
Data in XML | emd_36054_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_36054_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36054 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36054 | HTTPS FTP |
-Related structure data
Related structure data | 8j7zMC 8j5kC 8w4oC 8w4pC 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_36054.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_36054_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36054_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cm-FCP-trimer
Entire | Name: Cm-FCP-trimer |
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Components |
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-Supramolecule #1: Cm-FCP-trimer
Supramolecule | Name: Cm-FCP-trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Stephanocyclus meneghinianus (Diatom) |
-Macromolecule #1: FCP
Macromolecule | Name: FCP / type: protein_or_peptide / ID: 1 Details: fcp05 (fucoxanthin chlorophyll a/c binding protein 05) Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Stephanocyclus meneghinianus (Diatom) |
Molecular weight | Theoretical: 19.815451 KDa |
Sequence | String: AFEDELGAQP PLGFFDPFGM LSGDCTQERF DRLRYVEIKH GRIAQLAFLG QIVTRAGIHL PGSINYAGDS FDSFPNGVAA LFGPNSIPT AGLVQIIAFI GVLECAFMRD VPGTGNEHVG DFRNGYIDFG WDSFDEETKL QKRAIELNNG RAAMMGILGL M VHEEIIPL GYDPDLPIIG HLQ |
-Macromolecule #2: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...
Macromolecule | Name: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate type: ligand / ID: 2 / Number of copies: 21 / Formula: A86 |
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Molecular weight | Theoretical: 658.906 Da |
-Macromolecule #3: CHLOROPHYLL A
Macromolecule | Name: CHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 24 / Formula: CLA |
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Molecular weight | Theoretical: 893.489 Da |
Chemical component information | ChemComp-CLA: |
-Macromolecule #4: Chlorophyll c2
Macromolecule | Name: Chlorophyll c2 / type: ligand / ID: 4 / Number of copies: 6 / Formula: KC2 |
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Molecular weight | Theoretical: 608.926 Da |
Chemical component information | ChemComp-KC2: |
-Macromolecule #5: Chlorophyll c1
Macromolecule | Name: Chlorophyll c1 / type: ligand / ID: 5 / Number of copies: 3 / Formula: KC1 |
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Molecular weight | Theoretical: 610.941 Da |
Chemical component information | ChemComp-KC1: |
-Macromolecule #6: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Macromolecule | Name: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL type: ligand / ID: 6 / Number of copies: 3 / Formula: SQD |
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Molecular weight | Theoretical: 795.116 Da |
Chemical component information | ChemComp-SQD: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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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 |