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Yorodumi- EMDB-37268: Structure of PSII-FCPII-I/J/K complex in the PSII-FCPII supercomp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37268 | |||||||||
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Title | Structure of PSII-FCPII-I/J/K complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana | |||||||||
Map data | ||||||||||
Sample |
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Keywords | PSII-FCPII / PHOTOSYNTHESIS | |||||||||
Biological species | Stephanocyclus meneghinianus (Diatom) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 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_37268.map.gz | 256.8 MB | EMDB map data format | |
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Header (meta data) | emd-37268-v30.xml emd-37268.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37268_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_37268.png | 49.8 KB | ||
Filedesc metadata | emd-37268.cif.gz | 5.4 KB | ||
Others | emd_37268_half_map_1.map.gz emd_37268_half_map_2.map.gz | 474.3 MB 474.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37268 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37268 | HTTPS FTP |
-Related structure data
Related structure data | 8w4pMC 8j5kC 8j7zC 8w4oC 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_37268.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37268_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37268_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cm-PSII-FCPII-I/J/K
Entire | Name: Cm-PSII-FCPII-I/J/K |
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Components |
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-Supramolecule #1: Cm-PSII-FCPII-I/J/K
Supramolecule | Name: Cm-PSII-FCPII-I/J/K / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Cm-PSII-FCPII-I/J/K complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana |
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Source (natural) | Organism: Stephanocyclus meneghinianus (Diatom) |
-Macromolecule #1: FCPII-I, Fucoxanthin chlorophyll a/c binding protein
Macromolecule | Name: FCPII-I, Fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Stephanocyclus meneghinianus (Diatom) |
Molecular weight | Theoretical: 23.27917 KDa |
Sequence | String: SPRALPFGSA PATLDGSLVG DVGFDPIGFS TAPFASFNNP LYKEGDFMSD LEWLREAELT HGRIAQLAVL GFIWPALFGT FPGNENFGG ADAFSYVNPL EAITHVPDLA IYQIVGGMAW VEYQRVIRIK EQGKNRVSGD IGLGYPGGWN PFNLNYSPEE Y AEKQLQEI ...String: SPRALPFGSA PATLDGSLVG DVGFDPIGFS TAPFASFNNP LYKEGDFMSD LEWLREAELT HGRIAQLAVL GFIWPALFGT FPGNENFGG ADAFSYVNPL EAITHVPDLA IYQIVGGMAW VEYQRVIRIK EQGKNRVSGD IGLGYPGGWN PFNLNYSPEE Y AEKQLQEI KHCRLAMIGA FGLFFQALNS GTDIVSQLSP AFAAPDYAAK AGYFLP |
-Macromolecule #2: FCPII-K, Fucoxanthin chlorophyll a/c binding protein
Macromolecule | Name: FCPII-K, Fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Stephanocyclus meneghinianus (Diatom) |
Molecular weight | Theoretical: 13.039064 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) |
-Macromolecule #3: FCPII-J, Fucoxanthin chlorophyll a/c binding protein
Macromolecule | Name: FCPII-J, Fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Stephanocyclus meneghinianus (Diatom) |
Molecular weight | Theoretical: 17.850197 KDa |
Sequence | String: ENEIGALAPT GFFDPAKLSD GISQEKFDQY RLAELKHGRA AMLAVLGYVA PETYRFGYDL IPGELSTRDI PNGVAALNAI PFGGWVQMI AFVGTVEAYG WFTSPTGVLD LPADILAKRQ TSELQHGRLA MLAFLELIRH DSQNLAQPGF DGYDNLITGL P FLY |
-Macromolecule #4: CHLOROPHYLL A
Macromolecule | Name: CHLOROPHYLL A / type: ligand / ID: 4 / Number of copies: 30 / Formula: CLA |
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Molecular weight | Theoretical: 893.489 Da |
Chemical component information | ChemComp-CLA: |
-Macromolecule #5: (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: 5 / Number of copies: 6 / Formula: A86 |
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Molecular weight | Theoretical: 658.906 Da |
-Macromolecule #6: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...
Macromolecule | Name: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol type: ligand / ID: 6 / Number of copies: 2 / Formula: DD6 |
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Molecular weight | Theoretical: 582.855 Da |
Chemical component information | ChemComp-DD6: |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |