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Yorodumi- EMDB-30882: Photosystem I from a chlorophyll d-containing cyanobacterium Acar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30882 | |||||||||
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Title | Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina | |||||||||
Map data | ||||||||||
Sample |
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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 / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Acaryochloris marina MBIC11017 (bacteria) / Acaryochloris marinan MBIC11017 (bacteria) / Acaryochloris marina MBIC 11017 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Chen JH / Zhang X / Shen JR | |||||||||
Citation | Journal: J Integr Plant Biol / Year: 2021 Title: A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina. Authors: Caihuang Xu / Qingjun Zhu / Jing-Hua Chen / Liangliang Shen / Xiaohan Yi / Zihui Huang / Wenda Wang / Min Chen / Tingyun Kuang / Jian-Ren Shen / Xing Zhang / Guangye Han / Abstract: Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is ...Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A , A , and three Fe S clusters, F , F , and F . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light. | |||||||||
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_30882.map.gz | 230 MB | EMDB map data format | |
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Header (meta data) | emd-30882-v30.xml emd-30882.xml | 24.5 KB 24.5 KB | Display Display | EMDB header |
Images | emd_30882.png | 115.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30882 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30882 | HTTPS FTP |
-Validation report
Summary document | emd_30882_validation.pdf.gz | 456.1 KB | Display | EMDB validaton report |
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Full document | emd_30882_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | emd_30882_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_30882_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30882 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30882 | HTTPS FTP |
-Related structure data
Related structure data | 7dwqMC 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_30882.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.307 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 from a chlorophyll d-containing cyanobacterium Acar...
+Supramolecule #1: Photosystem I from a chlorophyll d-containing cyanobacterium Acar...
+Macromolecule #1: Photosystem I protein PsaD
+Macromolecule #2: Photosystem I P740 chlorophyll a apoprotein A1
+Macromolecule #3: Photosystem I P740 chlorophyll a apoprotein A2
+Macromolecule #4: Photosystem I iron-sulfur center
+Macromolecule #5: Photosystem I reaction center subunit IV
+Macromolecule #6: Photosystem I protein PsaF
+Macromolecule #7: Photosystem I reaction center subunit IX
+Macromolecule #8: Photosystem I protein PsaL
+Macromolecule #9: Photosystem I reaction center subunit XII
+Macromolecule #10: Photosystem I protein Psa27
+Macromolecule #11: CHLOROPHYLL D
+Macromolecule #12: PHYLLOQUINONE
+Macromolecule #13: IRON/SULFUR CLUSTER
+Macromolecule #14: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #15: CHLOROPHYLL D ISOMER
+Macromolecule #16: PHEOPHYTIN A
+Macromolecule #17: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...
+Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
-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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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Average exposure time: 10.0 sec. / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 2.5 µm / Calibrated magnification: 38244 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |