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Yorodumi- EMDB-36907: Cryo-EM structure of the RC-LH core comples from Halorhodospira h... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36907 | |||||||||
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Title | Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RC-LH complex / HALORHODOSPIRA HALOCHLORIS / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Halorhodospira halochloris (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.42 Å | |||||||||
Authors | Wang G-L / Qi C-H / Yu L-J | |||||||||
Funding support | China, 1 items
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Citation | Journal: J Integr Plant Biol / Year: 2024 Title: Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium, Halorhodospira halochloris. Authors: Chen-Hui Qi / Guang-Lei Wang / Fang-Fang Wang / Jie Wang / Xiang-Ping Wang / Mei-Juan Zou / Fei Ma / Michael T Madigan / Yukihiro Kimura / Zheng-Yu Wang-Otomo / Long-Jiang Yu / Abstract: Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center ...Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center (LH1-RC) core complex of this bacterium displays an LH1-Q transition at 1,016 nm, which is the lowest-energy wavelength absorption among all known phototrophs. Here we report the cryo-EM structure of the LH1-RC at 2.42 Å resolution. The LH1 complex forms a tricyclic ring structure composed of 16 αβγ-polypeptides and one αβ-heterodimer around the RC. From the cryo-EM density map, two previously unrecognized integral membrane proteins, referred to as protein G and protein Q, were identified. Both of these proteins are single transmembrane-spanning helices located between the LH1 ring and the RC L-subunit and are absent from the LH1-RC complexes of all other purple bacteria of which the structures have been determined so far. Besides bacteriochlorophyll b molecules (B1020) located on the periplasmic side of the Hlr. halochloris membrane, there are also two arrays of bacteriochlorophyll b molecules (B800 and B820) located on the cytoplasmic side. Only a single copy of a carotenoid (lycopene) was resolved in the Hlr. halochloris LH1-α3β3 and this was positioned within the complex. The potential quinone channel should be the space between the LH1-α3β3 that accommodates the single lycopene but does not contain a γ-polypeptide, B800 and B820. Our results provide a structural explanation for the unusual Q red shift and carotenoid absorption in the Hlr. halochloris spectrum and reveal new insights into photosynthetic mechanisms employed by a species that thrives under the harshest conditions of any phototrophic microorganism known. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36907.map.gz | 167.1 MB | EMDB map data format | |
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Header (meta data) | emd-36907-v30.xml emd-36907.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36907_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_36907.png | 53.1 KB | ||
Filedesc metadata | emd-36907.cif.gz | 7.8 KB | ||
Others | emd_36907_half_map_1.map.gz emd_36907_half_map_2.map.gz | 165.5 MB 165.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36907 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36907 | HTTPS FTP |
-Validation report
Summary document | emd_36907_validation.pdf.gz | 1016.2 KB | Display | EMDB validaton report |
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Full document | emd_36907_full_validation.pdf.gz | 1015.8 KB | Display | |
Data in XML | emd_36907_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | emd_36907_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36907 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36907 | HTTPS FTP |
-Related structure data
Related structure data | 8k5oMC 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_36907.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.02 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36907_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36907_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RC-LH core complex
+Supramolecule #1: RC-LH core complex
+Macromolecule #1: Photosynthetic reaction center cytochrome c subunit
+Macromolecule #2: Reaction center protein L chain
+Macromolecule #3: Reaction center protein M chain
+Macromolecule #4: Photosynthetic reaction center H subunit
+Macromolecule #5: Antenna complex alpha/beta subunit domain-containing protein
+Macromolecule #6: Light-harvesting LHI
+Macromolecule #7: Antenna complex alpha/beta subunit domain-containing protein
+Macromolecule #8: Beta subunit of light-harvesting 1
+Macromolecule #9: Gamma subunit of light-harvesting 1
+Macromolecule #10: reaction center small polypeptide
+Macromolecule #11: reactin center small polypeptide
+Macromolecule #12: HEME C
+Macromolecule #13: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #14: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #15: Trans-Geranyl Bacteriochlorophyll B
+Macromolecule #16: Trans-Geranyl Bacteriopheophytin B
+Macromolecule #17: Ubiquinone-8
+Macromolecule #18: UNKNOWN LIGAND
+Macromolecule #19: FE (III) ION
+Macromolecule #20: MENAQUINONE 8
+Macromolecule #21: CARDIOLIPIN
+Macromolecule #22: LYCOPENE
+Macromolecule #23: Trans-Geranyl 8-vinyl-bacteriochlorophyll B
+Macromolecule #24: DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
+Macromolecule #25: 2-O-octyl-beta-D-glucopyranose
-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 TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.8 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: 2.3000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |