+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15969 | ||||||||||||
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Title | Photosystem I assembly intermediate of Avena sativa | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | PSI structure / assembly intermediate / Monocotyledons / etiolation / PHOTOSYNTHESIS | ||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting / thylakoid membrane / chloroplast thylakoid / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis ...photosynthesis, light harvesting / thylakoid membrane / chloroplast thylakoid / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Avena sativa (oats) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||||||||
Authors | Naschberger A / Amunts A / Nelson N | ||||||||||||
Funding support | Sweden, Israel, 3 items
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Citation | Journal: To Be Published Title: Photosystem I assembly intermediate of Avena sativa Authors: Naschberger A / Amunts A / Nelson N | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15969.map.gz | 270.4 MB | EMDB map data format | |
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Header (meta data) | emd-15969-v30.xml emd-15969.xml | 32.7 KB 32.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15969_fsc.xml | 17.5 KB | Display | FSC data file |
Images | emd_15969.png | 123.1 KB | ||
Masks | emd_15969_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-15969.cif.gz | 9 KB | ||
Others | emd_15969_half_map_1.map.gz emd_15969_half_map_2.map.gz | 384.4 MB 384.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15969 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15969 | HTTPS FTP |
-Validation report
Summary document | emd_15969_validation.pdf.gz | 904.4 KB | Display | EMDB validaton report |
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Full document | emd_15969_full_validation.pdf.gz | 904 KB | Display | |
Data in XML | emd_15969_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | emd_15969_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15969 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15969 | HTTPS FTP |
-Related structure data
Related structure data | 8bcvMC 8bcwC 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_15969.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15969_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15969_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15969_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Assembly Intermediate of PSI from Avena sativa
+Supramolecule #1: Assembly Intermediate of PSI from Avena sativa
+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 VI
+Macromolecule #7: Photosystem I reaction center subunit VIII
+Macromolecule #8: Photosystem I reaction center subunit XI
+Macromolecule #9: Photosystem I reaction center subunit III
+Macromolecule #10: Photosystem I reaction center subunit V
+Macromolecule #11: Photosystem I reaction center subunit IX
+Macromolecule #12: Photosystem I reaction center subunit X
+Macromolecule #13: Chlorophyll a-b binding protein 1, chloroplastic
+Macromolecule #14: Chlorophyll a-b binding protein 2, chloroplastic
+Macromolecule #15: Chlorophyll a-b binding protein 3, chloroplastic
+Macromolecule #16: Chlorophyll a-b binding protein 4, chloroplastic
+Macromolecule #17: CHLOROPHYLL A ISOMER
+Macromolecule #18: CHLOROPHYLL A
+Macromolecule #19: PHYLLOQUINONE
+Macromolecule #20: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #21: BETA-CAROTENE
+Macromolecule #22: IRON/SULFUR CLUSTER
+Macromolecule #23: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #24: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #25: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #26: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #27: CHLOROPHYLL B
+Macromolecule #28: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #29: (1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...
+Macromolecule #30: Antheraxanthin
+Macromolecule #31: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.346 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: 2.1 µm / Nominal defocus min: 0.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |