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Yorodumi- EMDB-37642: The structure of PSI-CAC(L-14)of R.salina at 2.7 angstroms resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37642 | |||||||||
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Title | The structure of PSI-CAC(L-14)of R.salina at 2.7 angstroms resolution | |||||||||
Map data | ||||||||||
Sample |
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Keywords | thylakoid membrane / chlorophyll plastid / photosynthesis / oxyphototroph | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodomonas salina (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Zhang SM / Si L / Li M | |||||||||
Funding support | China, 2 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Growth phase-dependent reorganization of cryptophyte photosystem I antennae. Authors: Shumeng Zhang / Long Si / Xiaodong Su / Xuelin Zhao / Xiaomin An / Mei Li / Abstract: Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. ...Photosynthetic cryptophytes are eukaryotic algae that utilize membrane-embedded chlorophyll a/c binding proteins (CACs) and lumen-localized phycobiliproteins (PBPs) as their light-harvesting antennae. Cryptophytes go through logarithmic and stationary growth phases, and may adjust their light-harvesting capability according to their particular growth state. How cryptophytes change the type/arrangement of the photosynthetic antenna proteins to regulate their light-harvesting remains unknown. Here we solve four structures of cryptophyte photosystem I (PSI) bound with CACs that show the rearrangement of CACs at different growth phases. We identify a cryptophyte-unique protein, PsaQ, which harbors two chlorophyll molecules. PsaQ specifically binds to the lumenal region of PSI during logarithmic growth phase and may assist the association of PBPs with photosystems and energy transfer from PBPs to photosystems. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37642.map.gz | 17.2 MB | EMDB map data format | |
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Header (meta data) | emd-37642-v30.xml emd-37642.xml | 43.9 KB 43.9 KB | Display Display | EMDB header |
Images | emd_37642.png | 59.2 KB | ||
Filedesc metadata | emd-37642.cif.gz | 10.5 KB | ||
Others | emd_37642_half_map_1.map.gz emd_37642_half_map_2.map.gz | 141.1 MB 141.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37642 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37642 | HTTPS FTP |
-Validation report
Summary document | emd_37642_validation.pdf.gz | 872.6 KB | Display | EMDB validaton report |
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Full document | emd_37642_full_validation.pdf.gz | 872.2 KB | Display | |
Data in XML | emd_37642_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_37642_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37642 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37642 | HTTPS FTP |
-Related structure data
Related structure data | 8wm6MC 8wmjC 8wmvC 8wmwC 8wnwC 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_37642.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37642_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37642_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : PSI-CAC
+Supramolecule #1: PSI-CAC
+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
+Macromolecule #5: Photosystem I reaction center subunit IV
+Macromolecule #6: Photosystem I reaction center subunit III
+Macromolecule #7: Photosystem I reaction center subunit VIII
+Macromolecule #8: Photosystem I reaction center subunit IX
+Macromolecule #9: Photosystem I reaction center subunit XI
+Macromolecule #10: Photosystem I reaction center subunit XII
+Macromolecule #11: PsaO
+Macromolecule #12: Photosystem I reaction center subunit PsaK
+Macromolecule #13: chain s
+Macromolecule #14: cac-c
+Macromolecule #15: cac-a
+Macromolecule #16: cac-b
+Macromolecule #17: cac-h
+Macromolecule #18: cac-f
+Macromolecule #19: cac-e
+Macromolecule #20: cac-l
+Macromolecule #21: cac-k
+Macromolecule #22: cac-i
+Macromolecule #23: cac-d
+Macromolecule #24: cac-g
+Macromolecule #25: PsaR
+Macromolecule #26: cac-n
+Macromolecule #27: PsaQ
+Macromolecule #28: CHLOROPHYLL A
+Macromolecule #29: PHYLLOQUINONE
+Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #31: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tet...
+Macromolecule #32: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #33: IRON/SULFUR CLUSTER
+Macromolecule #34: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #35: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #36: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #37: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #38: Chlorophyll c2
+Macromolecule #39: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #40: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 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: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 86231 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |