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Yorodumi- EMDB-41434: Bottom cylinder of high-resolution phycobilisome quenched by OCP ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41434 | |||||||||||||||
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Title | Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement) | |||||||||||||||
Map data | refined map | |||||||||||||||
Sample |
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Keywords | Complex / light harvesting / pigment / PHOTOSYNTHESIS | |||||||||||||||
Function / homology | Function and homology information light absorption / Lyases / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity / photosynthesis / lyase activity Similarity search - Function | |||||||||||||||
Biological species | Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||||||||
Authors | Sauer PV / Sutter M / Cupellini L / Kirst H / Kerfeld CA | |||||||||||||||
Funding support | European Union, United States, Czech Republic, 4 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / ...Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / Eva Nogales / Tomáš Polívka / Benedetta Mennucci / Cheryl A Kerfeld / Abstract: Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) ...Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41434.map.gz | 255.3 MB | EMDB map data format | |
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Header (meta data) | emd-41434-v30.xml emd-41434.xml | 27.6 KB 27.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41434_fsc.xml | 16.8 KB | Display | FSC data file |
Images | emd_41434.png | 49.7 KB | ||
Masks | emd_41434_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-41434.cif.gz | 7.7 KB | ||
Others | emd_41434_additional_1.map.gz emd_41434_half_map_1.map.gz emd_41434_half_map_2.map.gz | 483.8 MB 475 MB 475 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41434 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41434 | HTTPS FTP |
-Validation report
Summary document | emd_41434_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_41434_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_41434_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | emd_41434_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41434 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41434 | HTTPS FTP |
-Related structure data
Related structure data | 8to2MC 8to5C 8tpjC 8troC 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_41434.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | refined map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.727 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41434_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: sharpened map
File | emd_41434_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41434_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41434_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
+Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
+Macromolecule #1: Phycobiliprotein ApcE
+Macromolecule #2: Orange carotenoid-binding protein
+Macromolecule #3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...
+Macromolecule #4: Allophycocyanin alpha chain
+Macromolecule #5: Allophycocyanin beta chain
+Macromolecule #6: Phycobilisome rod-core linker polypeptide CpcG
+Macromolecule #7: Allophycocyanin subunit alpha-B
+Macromolecule #8: Allophycocyanin subunit beta-18
+Macromolecule #9: Translation initiation factor IF-2
+Macromolecule #10: PHYCOCYANOBILIN
+Macromolecule #11: beta,beta-carotene-4,4'-dione
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.8 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |