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Yorodumi- EMDB-37513: Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37513 | |||||||||
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Title | Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information chloroplast thylakoid / plastoglobule / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...chloroplast thylakoid / plastoglobule / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / 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 / protein domain specific binding / mRNA binding / magnesium ion binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Fittonia albivenis (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
Authors | Huang GQ / Li XX / Sui SF / Qin XC | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI Authors: Huang GQ / Li XX / Sui SF / Qin XC | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37513.map.gz | 97.3 MB | EMDB map data format | |
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Header (meta data) | emd-37513-v30.xml emd-37513.xml | 35 KB 35 KB | Display Display | EMDB header |
Images | emd_37513.png | 154.1 KB | ||
Filedesc metadata | emd-37513.cif.gz | 9.2 KB | ||
Others | emd_37513_half_map_1.map.gz emd_37513_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37513 | HTTPS FTP |
-Validation report
Summary document | emd_37513_validation.pdf.gz | 1006.5 KB | Display | EMDB validaton report |
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Full document | emd_37513_full_validation.pdf.gz | 1006.1 KB | Display | |
Data in XML | emd_37513_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | emd_37513_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37513 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37513 | HTTPS FTP |
-Related structure data
Related structure data | 8wghMC 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_37513.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37513_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37513_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosystem I complex
+Supramolecule #1: Photosystem I complex
+Macromolecule #1: Chlorophyll a-b binding protein 1
+Macromolecule #2: Chlorophyll a-b binding protein 2
+Macromolecule #3: Chlorophyll a-b binding protein 3
+Macromolecule #4: Chlorophyll a-b binding protein 4
+Macromolecule #5: Photosystem I P700 chlorophyll a apoprotein A1
+Macromolecule #6: Photosystem I P700 chlorophyll a apoprotein A2
+Macromolecule #7: Photosystem I iron-sulfur center
+Macromolecule #8: Photosystem I reaction center subunit II
+Macromolecule #9: Photosystem I reaction center subunit IV
+Macromolecule #10: Photosystem I reaction center subunit III, chloroplastic
+Macromolecule #11: Photosystem I reaction center subunit VIII
+Macromolecule #12: Photosystem I reaction center subunit VI
+Macromolecule #13: Photosystem I reaction center subunit VIII
+Macromolecule #14: Photosystem I reaction center subunit IX
+Macromolecule #15: Photosystem I reaction center subunit psaK
+Macromolecule #16: Photosystem I reaction center subunit XI
+Macromolecule #17: Photosystem I reaction center subunit N
+Macromolecule #18: Photosystem I reaction center subunit O
+Macromolecule #19: CHLOROPHYLL B
+Macromolecule #20: CHLOROPHYLL A
+Macromolecule #21: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #22: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #23: BETA-CAROTENE
+Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #25: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #26: heptyl 1-thio-beta-D-glucopyranoside
+Macromolecule #27: PHYLLOQUINONE
+Macromolecule #28: IRON/SULFUR CLUSTER
+Macromolecule #29: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #30: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
-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 (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157342 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |