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Yorodumi- EMDB-14870: Monomeric PSI of Chlamydomonas reinhardtii at 2.31 A resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14870 | |||||||||||||||
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Title | Monomeric PSI of Chlamydomonas reinhardtii at 2.31 A resolution | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Function / homology | Function and homology information photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.31 Å | |||||||||||||||
Authors | Naschberger A / Amunts A | |||||||||||||||
Funding support | Sweden, Germany, 4 items
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Citation | Journal: Nat Plants / Year: 2022 Title: Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex. Authors: Andreas Naschberger / Laura Mosebach / Victor Tobiasson / Sebastian Kuhlgert / Martin Scholz / Annemarie Perez-Boerema / Thi Thu Hoai Ho / André Vidal-Meireles / Yuichiro Takahashi / ...Authors: Andreas Naschberger / Laura Mosebach / Victor Tobiasson / Sebastian Kuhlgert / Martin Scholz / Annemarie Perez-Boerema / Thi Thu Hoai Ho / André Vidal-Meireles / Yuichiro Takahashi / Michael Hippler / Alexey Amunts / Abstract: Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular ...Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Cryogenic electron microscopy identified that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI-light-harvesting complex I monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH and thus partially overlaps with the surface area that would bind one of the light-harvesting complex II complexes in state transitions. We also define the most accurate available PSI-light-harvesting complex I model at 2.3 Å resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations to all the pigments, as well as 621 water molecules that affect energy transfer pathways. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14870.map.gz | 274.8 MB | EMDB map data format | |
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Header (meta data) | emd-14870-v30.xml emd-14870.xml | 38 KB 38 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14870_fsc.xml | 17.5 KB | Display | FSC data file |
Images | emd_14870.png | 99.2 KB | ||
Masks | emd_14870_msk_1.map | 476.8 MB | Mask map | |
Others | emd_14870_half_map_1.map.gz emd_14870_half_map_2.map.gz | 384.9 MB 384.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14870 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14870 | HTTPS FTP |
-Validation report
Summary document | emd_14870_validation.pdf.gz | 788.1 KB | Display | EMDB validaton report |
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Full document | emd_14870_full_validation.pdf.gz | 787.7 KB | Display | |
Data in XML | emd_14870_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | emd_14870_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14870 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14870 | HTTPS FTP |
-Related structure data
Related structure data | 7zqcMC 7zq9C 7zqdC 7zqeC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14870.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14870_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14870_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14870_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosystem I dimer of Chlamydomonas reinhardtii
+Supramolecule #1: Photosystem I dimer of Chlamydomonas reinhardtii
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #3: Photosystem I iron-sulfur center
+Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic
+Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic
+Macromolecule #6: Photosystem I reaction center subunit III, chloroplastic
+Macromolecule #7: Photosystem I reaction center subunit V, chloroplastic
+Macromolecule #8: Photosystem I reaction center subunit VIII
+Macromolecule #9: Photosystem I reaction center subunit IX
+Macromolecule #10: PSI subunit V
+Macromolecule #11: Photosystem I reaction center subunit psaK, chloroplastic
+Macromolecule #12: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #13: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic (Lhca4)
+Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #20: CHLOROPHYLL A ISOMER
+Macromolecule #21: CHLOROPHYLL A
+Macromolecule #22: PHYLLOQUINONE
+Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #24: BETA-CAROTENE
+Macromolecule #25: IRON/SULFUR CLUSTER
+Macromolecule #26: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #27: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #28: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #29: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #30: CHLOROPHYLL B
+Macromolecule #31: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #32: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #33: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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: 45.8 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: 5.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |