+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33593 | |||||||||
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Title | Structure of the Anabaena PSI-monomer-IsiA supercomplex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Photosystem I / ELECTRON TRANSPORT / isiA / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / photosynthetic electron transport in photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Nostoc sp. (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Nagao R / Kato K / Hamaguchi T / Kawakami K / Yonekura K / Shen JR | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120. Authors: Ryo Nagao / Koji Kato / Tasuku Hamaguchi / Yoshifumi Ueno / Naoki Tsuboshita / Shota Shimizu / Miyu Furutani / Shigeki Ehira / Yoshiki Nakajima / Keisuke Kawakami / Takehiro Suzuki / Naoshi ...Authors: Ryo Nagao / Koji Kato / Tasuku Hamaguchi / Yoshifumi Ueno / Naoki Tsuboshita / Shota Shimizu / Miyu Furutani / Shigeki Ehira / Yoshiki Nakajima / Keisuke Kawakami / Takehiro Suzuki / Naoshi Dohmae / Seiji Akimoto / Koji Yonekura / Jian-Ren Shen / Abstract: Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property ...Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33593.map.gz | 13.1 MB | EMDB map data format | |
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Header (meta data) | emd-33593-v30.xml emd-33593.xml | 36.8 KB 36.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33593_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_33593.png | 162.3 KB | ||
Filedesc metadata | emd-33593.cif.gz | 8.6 KB | ||
Others | emd_33593_additional_1.map.gz emd_33593_half_map_1.map.gz emd_33593_half_map_2.map.gz | 43 MB 44.2 MB 44.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33593 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33593 | HTTPS FTP |
-Validation report
Summary document | emd_33593_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_33593_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_33593_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_33593_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33593 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33593 | HTTPS FTP |
-Related structure data
Related structure data | 7y3fMC 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_33593.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.99 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_33593_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_33593_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33593_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : PSI-monomer-IsiA
+Supramolecule #1: PSI-monomer-IsiA
+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: Unknown
+Macromolecule #10: PsaM
+Macromolecule #11: Photosystem I 4.8 kDa protein
+Macromolecule #12: Photosystem I reaction center subunit XI
+Macromolecule #13: IsiA
+Macromolecule #14: Iron stress-induced chlorophyll-binding protein
+Macromolecule #15: CHLOROPHYLL A ISOMER
+Macromolecule #16: CHLOROPHYLL A
+Macromolecule #17: PHYLLOQUINONE
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: BETA-CAROTENE
+Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #21: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #22: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #23: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.68 mg/mL | |||||||||
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Buffer | pH: 6.5 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 11.7 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: 1.8 µm / Nominal defocus min: 0.8 µm |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7y3f: |