+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9807 | |||||||||
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Title | Structure of PSI tetramer from Anabaena | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Kato K / Nagao R / Shen JR / Miyazaki N / Akita F | |||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structure of a cyanobacterial photosystem I tetramer revealed by cryo-electron microscopy. Authors: Koji Kato / Ryo Nagao / Tian-Yi Jiang / Yoshifumi Ueno / Makio Yokono / Siu Kit Chan / Mai Watanabe / Masahiko Ikeuchi / Jian-Ren Shen / Seiji Akimoto / Naoyuki Miyazaki / Fusamichi Akita / Abstract: Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a ...Photosystem I (PSI) functions to harvest light energy for conversion into chemical energy. The organisation of PSI is variable depending on the species of organism. Here we report the structure of a tetrameric PSI core isolated from a cyanobacterium, Anabaena sp. PCC 7120, analysed by single-particle cryo-electron microscopy (cryo-EM) at 3.3 Å resolution. The PSI tetramer has a C2 symmetry and is organised in a dimer of dimers form. The structure reveals interactions at the dimer-dimer interface and the existence of characteristic pigment orientations and inter-pigment distances within the dimer units that are important for unique excitation energy transfer. In particular, characteristic residues of PsaL are identified to be responsible for the formation of the tetramer. Time-resolved fluorescence analyses showed that the PSI tetramer has an enhanced excitation-energy quenching. These structural and spectroscopic findings provide insights into the physiological significance of the PSI tetramer and evolutionary changes of the PSI organisations. | |||||||||
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_9807.map.gz | 28.2 MB | EMDB map data format | |
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Header (meta data) | emd-9807-v30.xml emd-9807.xml | 26.6 KB 26.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9807_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_9807.png | 72 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9807 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9807 | HTTPS FTP |
-Related structure data
Related structure data | 6jeoMC 9877C 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_9807.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.12 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 : PSI tetramer
+Supramolecule #1: PSI tetramer
+Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2 1
+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 PsaK 1
+Macromolecule #10: Photosystem I reaction center subunit XI
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: Photosystem I 4.8 kDa protein
+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-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.014 mg/mL | ||||||
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Buffer | pH: 6.5 / Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |