+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31455 | |||||||||
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Title | Cryo-EM structure of a primordial cyanobacterial photosystem I | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity ...thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / chlorophyll binding / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gloeobacter violaceus PCC 7421 (bacteria) / Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.04 Å | |||||||||
Authors | Kato K / Hamaguchi T / Nagao R / Kawakami K / Yonekura K / Shen JR | |||||||||
Citation | Journal: Biorxiv / Year: 2022 Title: Structural basis for the absence of low-energy chlorophylls responsible for photoprotection from a primitive cyanobacterial PSI Authors: Kato K / Hamaguchi T / Nagao R / Kawakami K / Ueno Y / Suzuki T / Uchida H / Murakami A / Nakajima Y / Yokono M / Akimoto S / Dohmae N / Yonekura K / Shen JR | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31455.map.gz | 29.6 MB | EMDB map data format | |
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Header (meta data) | emd-31455-v30.xml emd-31455.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31455_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_31455.png | 197.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31455 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31455 | HTTPS FTP |
-Related structure data
Related structure data | 7f4vMC 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_31455.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.823 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : PSI trimer
+Supramolecule #1: PSI trimer
+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 Z
+Macromolecule #8: Unknown protein
+Macromolecule #9: Photosystem I reaction center subunit XI
+Macromolecule #10: Photosystem I reaction center subunit XII
+Macromolecule #11: CHLOROPHYLL A ISOMER
+Macromolecule #12: CHLOROPHYLL A
+Macromolecule #13: Menaquinone-4
+Macromolecule #14: IRON/SULFUR CLUSTER
+Macromolecule #15: BETA-CAROTENE
+Macromolecule #16: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #17: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #18: 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 R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE | ||||||
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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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: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 70.22 e/Å2 |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7f4v: |