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Yorodumi- PDB-8k5o: Cryo-EM structure of the RC-LH core comples from Halorhodospira h... -
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-Basic information
Entry | Database: PDB / ID: 8k5o | ||||||
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Title | Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / RC-LH complex / HALORHODOSPIRA HALOCHLORIS | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å | ||||||
Authors | Wang, G.-L. / Qi, C.-H. / Yu, L.-J. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k5o.cif.gz | 853.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k5o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8k5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k5o_validation.pdf.gz | 7.2 MB | Display | wwPDB validaton report |
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Full document | 8k5o_full_validation.pdf.gz | 7.4 MB | Display | |
Data in XML | 8k5o_validation.xml.gz | 188.8 KB | Display | |
Data in CIF | 8k5o_validation.cif.gz | 234.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/8k5o ftp://data.pdbj.org/pub/pdb/validation_reports/k5/8k5o | HTTPS FTP |
-Related structure data
Related structure data | 36907MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosynthetic reaction center ... , 2 types, 2 molecules CH
#1: Protein | Mass: 41612.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X829 |
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#4: Protein | Mass: 31293.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X838 |
-Reaction center protein ... , 2 types, 2 molecules LM
#2: Protein | Mass: 31115.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8XAH6 |
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#3: Protein | Mass: 36221.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X847 |
-Antenna complex alpha/beta subunit domain-containing ... , 2 types, 17 molecules 4wYbkntz6FKPSVehq
#5: Protein | Mass: 12053.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A110B4Z6 |
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#7: Protein | Mass: 7696.815 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8XBE4 |
-Protein , 2 types, 17 molecules 3xZclou17GNQTWfir
#6: Protein | Mass: 7562.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A120MZP7 |
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#8: Protein | Mass: 9555.675 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X9B2 |
-Protein/peptide , 3 types, 18 molecules vXajmsy58IORUdgp29
#9: Protein/peptide | Mass: 3123.757 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) #10: Protein/peptide | | Mass: 3531.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) #11: Protein/peptide | | Mass: 3762.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) |
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-Sugars , 1 types, 2 molecules
#25: Sugar |
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-Non-polymers , 13 types, 193 molecules
#12: Chemical | ChemComp-HEC / #13: Chemical | ChemComp-PGV / ( #14: Chemical | ChemComp-LHG / | #15: Chemical | ChemComp-A1LZM / Mass: 907.472 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION #16: Chemical | Mass: 885.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72N4O6 / Feature type: SUBJECT OF INVESTIGATION #17: Chemical | ChemComp-UQ8 / | #18: Chemical | ChemComp-UNL / Mass: 909.488 Da / Num. of mol.: 57 / Source method: obtained synthetically #19: Chemical | ChemComp-FE / | #20: Chemical | #21: Chemical | #22: Chemical | ChemComp-LYC / | #23: Chemical | ChemComp-A1LZQ / Mass: 907.472 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION #24: Chemical | ChemComp-PEF / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RC-LH core complex / Type: COMPLEX / Entity ID: #1, #3-#11 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Halorhodospira halochloris (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 60.8 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.19.2_4158: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353518 / Symmetry type: POINT | ||||||||||||||||||||||||
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