+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15970 | ||||||||||||
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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 thylakoid membrane / chloroplast thylakoid / photosystem I / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding ...thylakoid membrane / chloroplast thylakoid / photosystem I / photosystem I / 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: 2.11 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_15970.map.gz | 148.1 MB | EMDB map data format | |
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Header (meta data) | emd-15970-v30.xml emd-15970.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15970_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_15970.png | 80.8 KB | ||
Masks | emd_15970_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-15970.cif.gz | 7.4 KB | ||
Others | emd_15970_half_map_1.map.gz emd_15970_half_map_2.map.gz | 195.6 MB 195.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15970 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15970 | HTTPS FTP |
-Validation report
Summary document | emd_15970_validation.pdf.gz | 866.2 KB | Display | EMDB validaton report |
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Full document | emd_15970_full_validation.pdf.gz | 865.7 KB | Display | |
Data in XML | emd_15970_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_15970_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15970 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15970 | HTTPS FTP |
-Related structure data
Related structure data | 8bcwMC 8bcvC 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_15970.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: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15970_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15970_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15970_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, chloroplastic
+Macromolecule #5: Photosystem I reaction center subunit IV A, chloroplastic
+Macromolecule #6: Photosystem I reaction center subunit VI, chloroplastic
+Macromolecule #7: Photosystem I reaction center subunit VIII
+Macromolecule #8: PSI subunit V
+Macromolecule #9: CHLOROPHYLL A ISOMER
+Macromolecule #10: CHLOROPHYLL A
+Macromolecule #11: PHYLLOQUINONE
+Macromolecule #12: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #13: BETA-CAROTENE
+Macromolecule #14: IRON/SULFUR CLUSTER
+Macromolecule #15: DODECYL-ALPHA-D-MALTOSIDE
+Macromolecule #16: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #17: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #18: 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 |