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Yorodumi- EMDB-33568: PSII-d3 of PBS-PSII-PSI-LHCs megacomplex from Porphyridium purpureum. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33568 | |||||||||
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Title | PSII-d3 of PBS-PSII-PSI-LHCs megacomplex from Porphyridium purpureum. | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Porphyridium purpureum (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | You X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Structure of lateral hexamer of PBS-PSII-PSI-LHCs megacomplex at 6.3 Angstroms resolution. Authors: You X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33568.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-33568-v30.xml emd-33568.xml | 43.6 KB 43.6 KB | Display Display | EMDB header |
Images | emd_33568.png | 109.9 KB | ||
Others | emd_33568_half_map_1.map.gz emd_33568_half_map_2.map.gz | 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33568 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33568 | HTTPS FTP |
-Validation report
Summary document | emd_33568_validation.pdf.gz | 904.8 KB | Display | EMDB validaton report |
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Full document | emd_33568_full_validation.pdf.gz | 904.4 KB | Display | |
Data in XML | emd_33568_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_33568_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33568 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33568 | HTTPS FTP |
-Related structure data
Related structure data | 7y1o 8jngC 8jnlC 8jnmC 8jnnC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33568.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.632 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33568_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33568_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Lateral hexamer of PBS
+Supramolecule #1: Lateral hexamer of PBS
+Macromolecule #1: Photosystem II protein D1
+Macromolecule #2: Photosystem II CP47 reaction center protein
+Macromolecule #3: Photosystem II CP43 reaction center protein
+Macromolecule #4: Photosystem II D2 protein
+Macromolecule #5: Cytochrome b559 subunit alpha
+Macromolecule #6: Cytochrome b559 subunit beta
+Macromolecule #7: PSII_Pbs31 domain-containing protein
+Macromolecule #8: Photosystem II reaction center protein H
+Macromolecule #9: Photosystem II reaction center protein I
+Macromolecule #10: Photosystem II reaction center protein J
+Macromolecule #11: Photosystem II reaction center protein K
+Macromolecule #12: Photosystem II reaction center protein L
+Macromolecule #13: PsbM
+Macromolecule #14: Psb34
+Macromolecule #15: Oxygen-evolving enhancer protein
+Macromolecule #16: PsbQ'
+Macromolecule #17: Photosystem II protein Y
+Macromolecule #18: LPP1
+Macromolecule #19: Photosystem II reaction center protein T
+Macromolecule #20: PS II complex 12 kDa extrinsic protein
+Macromolecule #21: Cytochrome c550
+Macromolecule #22: Photosystem II reaction center Psb28 protein
+Macromolecule #23: Photosystem II reaction center X protein
+Macromolecule #24: Photosystem II reaction center protein Ycf12
+Macromolecule #25: Photosystem II reaction center protein Z
+Macromolecule #26: CNT
+Macromolecule #27: CNT
+Macromolecule #28: CNT
+Macromolecule #29: BETA-CAROTENE
+Macromolecule #30: CHLORIDE ION
+Macromolecule #31: CHLOROPHYLL A
+Macromolecule #32: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #33: CA-MN4-O5 CLUSTER
+Macromolecule #34: FE (III) ION
+Macromolecule #35: PHEOPHYTIN A
+Macromolecule #36: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #37: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #38: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #39: BICARBONATE ION
+Macromolecule #40: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #41: GLYCEROL
+Macromolecule #42: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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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: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |