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- EMDB-37268: Structure of PSII-FCPII-I/J/K complex in the PSII-FCPII supercomp... -
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Open data
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Basic information
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Title | Structure of PSII-FCPII-I/J/K complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana | |||||||||
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![]() | PSII-FCPII / PHOTOSYNTHESIS | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
![]() | Shen LL / Li ZH / Shen JR / Wang WD | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 256.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.9 KB | Display | ![]() |
Images | ![]() | 49.8 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 474.3 MB 474.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8w4pMC ![]() 8j5kC ![]() 8j7zC ![]() 8w4oC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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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 |
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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: ![]() |
-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: ![]() |
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: ![]() |
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: ![]() |
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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![]() | 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 K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |