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Yorodumi- EMDB-9918: Cryo-EM structure of the tetrameric photosystem I from a heterocy... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9918 | |||||||||
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Title | Cryo-EM structure of the tetrameric photosystem I from a heterocyst-forming cyanobacterium Anabaena sp. PCC7120 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Photosystem I / PSI / PCC7120 / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.37 Å | |||||||||
Authors | Zheng L / Li Y | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Plants / Year: 2019 Title: Structural and functional insights into the tetrameric photosystem I from heterocyst-forming cyanobacteria. Authors: Lvqin Zheng / Yanbing Li / Xiying Li / Qinglu Zhong / Ningning Li / Kun Zhang / Yuebin Zhang / Huiying Chu / Chengying Ma / Guohui Li / Jindong Zhao / Ning Gao / Abstract: Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric ...Two large protein-cofactor complexes, photosystem I and photosystem II, are the central components of photosynthesis in the thylakoid membranes. Here, we report the 2.37-Å structure of a tetrameric photosystem I complex from a heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. Four photosystem I monomers, organized in a dimer of dimer, form two distinct interfaces that are largely mediated by specifically orientated polar lipids, such as sulfoquinovosyl diacylglycerol. The structure depicts a more closely connected network of chlorophylls across monomer interfaces than those seen in trimeric PSI from thermophilic cyanobacteria, possibly allowing a more efficient energy transfer between monomers. Our physiological data also revealed a functional link of photosystem I oligomerization to cyclic electron flow and thylakoid membrane organization. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9918.map.gz | 227.4 MB | EMDB map data format | |
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Header (meta data) | emd-9918-v30.xml emd-9918.xml | 25 KB 25 KB | Display Display | EMDB header |
Images | emd_9918.png | 111.5 KB | ||
Filedesc metadata | emd-9918.cif.gz | 7.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9918 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9918 | HTTPS FTP |
-Validation report
Summary document | emd_9918_validation.pdf.gz | 685.2 KB | Display | EMDB validaton report |
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Full document | emd_9918_full_validation.pdf.gz | 684.8 KB | Display | |
Data in XML | emd_9918_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_9918_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9918 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9918 | HTTPS FTP |
-Related structure data
Related structure data | 6k61MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9918.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.052 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Photosystem I complex of cyanobacterium Anabaena sp. PCC 7120
+Supramolecule #1: Photosystem I complex of cyanobacterium Anabaena sp. PCC 7120
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I 4.8 kDa protein
+Macromolecule #3: Photosystem I P700 chlorophyll a apoprotein A2 1
+Macromolecule #4: Photosystem I iron-sulfur center
+Macromolecule #5: Photosystem I reaction center subunit II
+Macromolecule #6: Photosystem I reaction center subunit IV
+Macromolecule #7: Photosystem I reaction center subunit III
+Macromolecule #8: Photosystem I reaction center subunit IX
+Macromolecule #9: Photosystem I reaction center subunit PsaK 1
+Macromolecule #10: Photosystem I reaction center subunit VIII
+Macromolecule #11: Photosystem I reaction center subunit XI
+Macromolecule #12: Photosystem I reaction center subunit XII
+Macromolecule #13: CHLOROPHYLL A ISOMER
+Macromolecule #14: CHLOROPHYLL A
+Macromolecule #15: PHYLLOQUINONE
+Macromolecule #16: IRON/SULFUR CLUSTER
+Macromolecule #17: BETA-CAROTENE
+Macromolecule #18: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #19: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-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: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71600 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |