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Yorodumi- EMDB-38455: Structure of inactive Photosystem II associated with CAC antenna ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38455 | |||||||||
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Title | Structure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina | |||||||||
Map data | Composite map of PSII-CAC supercomplex from Rhodomonas Salina | |||||||||
Sample |
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Keywords | Photosystem II associated with CAC antenna from Rhodomonas Salina / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding ...photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / chloroplast thylakoid membrane / photosynthetic electron transport in photosystem II / photosynthesis / electron transfer activity / oxidoreductase activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodomonas salina (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.57 Å | |||||||||
Authors | Si L / Li M | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure of inactive Photosystem II associated with CAC antenna from Rhodomonas Salina Authors: Si L / Li M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38455.map.gz | 9.1 MB | EMDB map data format | |
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Header (meta data) | emd-38455-v30.xml emd-38455.xml | 36.9 KB 36.9 KB | Display Display | EMDB header |
Images | emd_38455.png | 126.8 KB | ||
Filedesc metadata | emd-38455.cif.gz | 9.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38455 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38455 | HTTPS FTP |
-Validation report
Summary document | emd_38455_validation.pdf.gz | 400.5 KB | Display | EMDB validaton report |
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Full document | emd_38455_full_validation.pdf.gz | 400.1 KB | Display | |
Data in XML | emd_38455_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_38455_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38455 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38455 | HTTPS FTP |
-Related structure data
Related structure data | 8xlpMC C: citing same article (ref.) M: atomic model generated by this map |
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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_38455.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of PSII-CAC supercomplex from Rhodomonas Salina | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04003 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Inactive Photosystem II associated with chlorophyll a/c binding p...
+Supramolecule #1: Inactive Photosystem II associated with chlorophyll a/c binding p...
+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: Photosystem II reaction center protein H
+Macromolecule #8: Photosystem II reaction center protein I
+Macromolecule #9: Photosystem II reaction center protein K
+Macromolecule #10: Photosystem II reaction center protein L
+Macromolecule #11: Photosystem II protein M
+Macromolecule #12: Photosystem II reaction center protein T
+Macromolecule #13: Photosystem II protein W
+Macromolecule #14: Photosystem II reaction center X protein
+Macromolecule #15: Photosystem II reaction center protein Psb30
+Macromolecule #16: Photosystem II reaction center protein Z
+Macromolecule #17: NCP
+Macromolecule #18: CAC2
+Macromolecule #19: CAC3
+Macromolecule #20: CAC4
+Macromolecule #21: CAC5
+Macromolecule #22: CAC6
+Macromolecule #23: CAC1
+Macromolecule #24: FE (II) ION
+Macromolecule #25: CHLOROPHYLL A
+Macromolecule #26: PHEOPHYTIN A
+Macromolecule #27: 1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tet...
+Macromolecule #28: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #29: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #30: BICARBONATE ION
+Macromolecule #31: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #32: CHLORIDE ION
+Macromolecule #33: MANGANESE (II) ION
+Macromolecule #34: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #36: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #37: Chlorophyll c2
+Macromolecule #38: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #39: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #40: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 60.0 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: 2.2 µm / Nominal defocus min: 1.2 µm |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112613 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |