+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0524 | |||||||||
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Title | The structure of the photosystem I IsiA super-complex | |||||||||
Map data | PSI-IsiA super-complex from cyanobacteria | |||||||||
Sample |
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Keywords | Photosystem / Antenna / Chlorophyll / Membrane / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis ...plasma membrane-derived photosystem I / cellular response to iron ion starvation / photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / 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 | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Toporik H / Li J | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: The structure of the stress-induced photosystem I-IsiA antenna supercomplex. Authors: Hila Toporik / Jin Li / Dewight Williams / Po-Lin Chiu / Yuval Mazor / Abstract: Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with ...Photochemical conversion in oxygenic photosynthesis takes place in two large protein-pigment complexes named photosystem II and photosystem I (PSII and PSI, respectively). Photosystems associate with antennae in vivo to increase the size of photosynthetic units to hundreds or thousands of pigments. Regulation of the interactions between antennae and photosystems allows photosynthetic organisms to adapt to their environment. In low-iron environments, cyanobacteria express IsiA, a PSI antenna, critical to their survival. Here we describe the structure of the PSI-IsiA complex isolated from the mesophilic cyanobacterium Synechocystis sp. PCC 6803. This 2-MDa photosystem-antenna supercomplex structure reveals more than 700 pigments coordinated by 51 subunits, as well as the mechanisms facilitating the self-assembly and association of IsiA with multiple PSI assemblies. | |||||||||
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_0524.map.gz | 39.4 MB | EMDB map data format | |
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Header (meta data) | emd-0524-v30.xml emd-0524.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0524_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_0524.png | 78.6 KB | ||
Filedesc metadata | emd-0524.cif.gz | 7.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0524 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0524 | HTTPS FTP |
-Validation report
Summary document | emd_0524_validation.pdf.gz | 438 KB | Display | EMDB validaton report |
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Full document | emd_0524_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | emd_0524_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | emd_0524_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0524 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0524 | HTTPS FTP |
-Related structure data
Related structure data | 6nwaMC 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_0524.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PSI-IsiA super-complex from cyanobacteria | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.024 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-IsiA
+Supramolecule #1: PSI-IsiA
+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: Iron stress-induced chlorophyll-binding protein
+Macromolecule #12: Photosystem I reaction center subunit PsaK 1
+Macromolecule #13: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #14: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #15: CHLOROPHYLL A ISOMER
+Macromolecule #16: CHLOROPHYLL A
+Macromolecule #17: PHYLLOQUINONE
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: BETA-CAROTENE
+Macromolecule #20: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #21: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / 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: 1.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 16.43 |
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Output model | PDB-6nwa: |