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Yorodumi- EMDB-10558: Cryo- EM structure of the Thermosynechococcus elongatus photosyst... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10558 | ||||||||||||
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Title | Cryo- EM structure of the Thermosynechococcus elongatus photosystem I in the presence of cytochrome c6 | ||||||||||||
Map data | Structure of photosystem I from Thermosynechococcus elongatus | ||||||||||||
Sample |
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Function / homology | Function and homology information photosystem I reaction center / photosystem I / photosystem I / 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 ...photosystem I reaction center / photosystem I / photosystem I / 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 / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Thermosynechococcus elongatus BP-1 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||||||||
Authors | Koelsch A / Radon C / Baumert A / Buerger J / Mielke T / Lisdat F / Zouni A / Wendler P | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Curr.Opin.Struct.Biol. / Year: 2020 Title: Current limits of structural biology: The transient interaction between cytochrome c6 and photosystem I Authors: Koelsch A / Radon C / Golub M / Baumert A / Burger J / Miehlke T / Lisdat F / Feoktystov A / Pieper J / Zouni A / Wendler P | ||||||||||||
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_10558.map.gz | 77.4 MB | EMDB map data format | |
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Header (meta data) | emd-10558-v30.xml emd-10558.xml | 28 KB 28 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10558_fsc.xml | 19.9 KB | Display | FSC data file |
Images | emd_10558.png | 99.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10558 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10558 | HTTPS FTP |
-Validation report
Summary document | emd_10558_validation.pdf.gz | 274.7 KB | Display | EMDB validaton report |
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Full document | emd_10558_full_validation.pdf.gz | 273.9 KB | Display | |
Data in XML | emd_10558_validation.xml.gz | 17.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10558 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10558 | HTTPS FTP |
-Related structure data
Related structure data | 6trcMC 6traC 6trdC 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_10558.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of photosystem I from Thermosynechococcus elongatus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.628 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 : photosystem I
+Supramolecule #1: photosystem I
+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 PsaK
+Macromolecule #10: Photosystem I reaction center subunit XI
+Macromolecule #11: Photosystem I reaction center subunit XII
+Macromolecule #12: Photosystem I 4.8K protein
+Macromolecule #13: CHLOROPHYLL A ISOMER
+Macromolecule #14: CHLOROPHYLL A
+Macromolecule #15: PHYLLOQUINONE
+Macromolecule #16: BETA-CAROTENE
+Macromolecule #17: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: CALCIUM ION
+Macromolecule #20: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #21: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE | ||||||||||||
Details | Photosystem I was crosslinked with its electron donor cytochrome c6. Crosslinked particles are monodisperse. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 32.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-6trc: |