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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30820 | |||||||||
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Title | Structure of Wild-type PSI monomer1 from Cyanophora paradoxa | |||||||||
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Function / homology | ![]() cyanelle thylakoid membrane / thylakoid membrane / chloroplast thylakoid / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...cyanelle thylakoid membrane / thylakoid membrane / chloroplast thylakoid / photosystem I reaction center / photosystem I / photosystem I / plastid / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Kato K / Nagao R / Akita F / Miyazaki N / Shen JR | |||||||||
![]() | ![]() Title: Structural insights into an evolutionary turning-point of photosystem I from prokaryotes to eukaryotes Authors: Kato K / Nagao R / Ueno Y / Yokono M / Suzuki T / Jiang TY / Dohmae N / Akita F / Akimoto S / Miyazaki N / Shen JR | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 29.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.4 KB 24.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 42.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 381.6 KB | Display | ![]() |
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Full document | ![]() | 381.2 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dr0MC ![]() 7dr1C ![]() 7dr2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.093 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : PSI monomer1
+Supramolecule #1: PSI monomer1
+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, cyanelle
+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: CHLOROPHYLL A ISOMER
+Macromolecule #13: CHLOROPHYLL A
+Macromolecule #14: PHYLLOQUINONE
+Macromolecule #15: IRON/SULFUR CLUSTER
+Macromolecule #16: BETA-CAROTENE
+Macromolecule #17: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #18: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.007 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 / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
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Output model | ![]() PDB-7dr0: |