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Yorodumi- EMDB-28962: LH2-LH3 antenna in antiparallel configuration embedded in a nanodisc -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28962 | ||||||||||||||||||
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Title | LH2-LH3 antenna in antiparallel configuration embedded in a nanodisc | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | antenna / membrane protein / nanodisc / bacteriochlorophyll / PHOTOSYNTHESIS | ||||||||||||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Magnetospirillum molischianum (magnetotactic) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.4 Å | ||||||||||||||||||
Authors | Toporik H / Harris D / Schlau-Cohen GS / Mazor Y | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria. Authors: Dihao Wang / Olivia C Fiebig / Dvir Harris / Hila Toporik / Yi Ji / Chern Chuang / Muath Nairat / Ashley L Tong / John I Ogren / Stephanie M Hart / Jianshu Cao / James N Sturgis / Yuval ...Authors: Dihao Wang / Olivia C Fiebig / Dvir Harris / Hila Toporik / Yi Ji / Chern Chuang / Muath Nairat / Ashley L Tong / John I Ogren / Stephanie M Hart / Jianshu Cao / James N Sturgis / Yuval Mazor / Gabriela S Schlau-Cohen / Abstract: In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical ...In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28962.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-28962-v30.xml emd-28962.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_28962.png | 30 KB | ||
Filedesc metadata | emd-28962.cif.gz | 5.3 KB | ||
Others | emd_28962_half_map_1.map.gz emd_28962_half_map_2.map.gz | 9.8 MB 9.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28962 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28962 | HTTPS FTP |
-Validation report
Summary document | emd_28962_validation.pdf.gz | 750.6 KB | Display | EMDB validaton report |
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Full document | emd_28962_full_validation.pdf.gz | 750.2 KB | Display | |
Data in XML | emd_28962_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_28962_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28962 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28962 | HTTPS FTP |
-Related structure data
Related structure data | 8fb9MC 7tuwC 7tv3C 8fbbC 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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-Map
File | Download / File: emd_28962.map.gz / Format: CCP4 / Size: 12.9 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: 1.75 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28962_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28962_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : LHII-LHIII complex in nanodisk
Entire | Name: LHII-LHIII complex in nanodisk |
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Components |
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-Supramolecule #1: LHII-LHIII complex in nanodisk
Supramolecule | Name: LHII-LHIII complex in nanodisk / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Magnetospirillum molischianum (magnetotactic) |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Light-harvesting protein B800-820 alpha chain
Macromolecule | Name: Light-harvesting protein B800-820 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Magnetospirillum molischianum (magnetotactic) |
Molecular weight | Theoretical: 6.08812 KDa |
Sequence | String: SNPKDDYKIW LVINPSTWLP VIWIVALLTA IAVHSFVLSV PGYNFLASAA AKTAAK UniProtKB: Light-harvesting protein B800-820 alpha chain |
-Macromolecule #2: Light-harvesting protein B800-820 beta chain
Macromolecule | Name: Light-harvesting protein B800-820 beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Magnetospirillum molischianum (magnetotactic) |
Molecular weight | Theoretical: 5.120873 KDa |
Sequence | String: AERSLSGLTE EEAVAVHDQF KTTFSAFILL AAVAHVLVWI WKPWF UniProtKB: Light-harvesting protein B800-820 beta chain |
-Macromolecule #3: Light-harvesting protein B-800/850 alpha chain
Macromolecule | Name: Light-harvesting protein B-800/850 alpha chain / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Magnetospirillum molischianum (magnetotactic) |
Molecular weight | Theoretical: 5.94498 KDa |
Sequence | String: SNPKDDYKIW LVINPSTWLP VIWIVATVVA IAVHAAVLAA PGFNWIALGA AKSAAK UniProtKB: Light-harvesting protein B-800/850 alpha chain |
-Macromolecule #4: Light-harvesting protein B-800/850 beta 1 chain
Macromolecule | Name: Light-harvesting protein B-800/850 beta 1 chain / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Magnetospirillum molischianum (magnetotactic) |
Molecular weight | Theoretical: 5.120873 KDa |
Sequence | String: AERSLSGLTE EEAIAVHDQF KTTFSAFIIL AAVAHVLVWV WKPWF UniProtKB: Light-harvesting protein B-800/850 beta 1 chain |
-Macromolecule #5: BACTERIOCHLOROPHYLL A
Macromolecule | Name: BACTERIOCHLOROPHYLL A / type: ligand / ID: 5 / Number of copies: 48 / Formula: BCL |
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Molecular weight | Theoretical: 911.504 Da |
Chemical component information | ChemComp-BCL: |
-Macromolecule #6: LYCOPENE
Macromolecule | Name: LYCOPENE / type: ligand / ID: 6 / Number of copies: 16 / Formula: LYC |
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Molecular weight | Theoretical: 536.873 Da |
Chemical component information | ChemComp-LYC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
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: 75.0 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: 2.5 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63637 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-8fb9: |