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Yorodumi- PDB-8iug: Cryo-EM structure of the RC-LH core complex from roseiflexus cast... -
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-Basic information
Entry | Database: PDB / ID: 8iug | ||||||||||||
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Title | Cryo-EM structure of the RC-LH core complex from roseiflexus castenholzii | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / RC-LH complex / ROSEIFLEXUS CASTENHOLZII | ||||||||||||
Function / homology | Function and homology information organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / chlorophyll binding / 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 light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / chlorophyll binding / 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 | Roseiflexus castenholzii (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||||||||
Authors | Wang, G.-L. / Qi, C.-H. / Yu, L.-J. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J Biol Chem / Year: 2023 Title: New insights on the photocomplex of Roseiflexus castenholzii revealed from comparisons of native and carotenoid-depleted complexes. Authors: Chen-Hui Qi / Guang-Lei Wang / Fang-Fang Wang / Yueyong Xin / Mei-Juan Zou / Michael T Madigan / Zheng-Yu Wang-Otomo / Fei Ma / Long-Jiang Yu / Abstract: In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. ...In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. Diphenylamine (DPA) inhibits carotenogenesis but not phototrophic growth of anoxygenic phototrophs and eliminates virtually all Crts from photocomplexes. To investigate the effect of Crts on assembly of the reaction center-light-harvesting (RC-LH) complex from the filamentous anoxygenic phototroph Roseiflexus (Rfl.) castenholzii, we generated carotenoidless (Crt-less) RC-LH complexes by growing cells in the presence of DPA. Here, we present cryo-EM structures of the Rfl. castenholzii native and Crt-less RC-LH complexes with resolutions of 2.86 Å and 2.85 Å, respectively. From the high-quality map obtained, several important but previously unresolved details in the Rfl. castenholzii RC-LH structure were determined unambiguously including the assignment and likely function of three small polypeptides, and the content and spatial arrangement of Crts with bacteriochlorophyll molecules. The overall structures of Crt-containing and Crt-less complexes are similar. However, structural comparisons showed that only five Crts remain in complexes from DPA-treated cells and that the subunit X (TMx) flanked on the N-terminal helix of the Cyt-subunit is missing. Based on these results, the function of Crts in the assembly of the Rfl. castenholzii RC-LH complex and the molecular mechanism of quinone exchange is discussed. These structural details provide a fresh look at the photosynthetic apparatus of an evolutionary ancient phototroph as well as new insights into the importance of Crts for proper assembly and functioning of the RC-LH complex. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iug.cif.gz | 569.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iug.ent.gz | 491.5 KB | Display | PDB format |
PDBx/mmJSON format | 8iug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iug_validation.pdf.gz | 5.4 MB | Display | wwPDB validaton report |
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Full document | 8iug_full_validation.pdf.gz | 5.8 MB | Display | |
Data in XML | 8iug_validation.xml.gz | 149.5 KB | Display | |
Data in CIF | 8iug_validation.cif.gz | 178.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/8iug ftp://data.pdbj.org/pub/pdb/validation_reports/iu/8iug | HTTPS FTP |
-Related structure data
Related structure data | 35721MC 8iunC 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
-Protein , 3 types, 18 molecules 02468BEGIKOQSUWCLM
#1: Protein | Mass: 6432.513 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: A7NQE9 #3: Protein | | Mass: 34923.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XC9 #4: Protein | Mass: 71707.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD0 |
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-Protein/peptide , 3 types, 17 molecules 13579ADFHJNPRTVXZ
#2: Protein/peptide | Mass: 4724.656 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD1 #5: Protein/peptide | | Mass: 3384.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) #7: Protein/peptide | | Mass: 740.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) |
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-Reaction center small ... , 2 types, 2 molecules Yh
#6: Protein/peptide | Mass: 4493.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) |
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#8: Protein | Mass: 6927.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) |
-Sugars , 2 types, 16 molecules
#12: Sugar | #13: Sugar | ChemComp-BGL / |
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-Non-polymers , 12 types, 117 molecules
#9: Chemical | ChemComp-BCL / #10: Chemical | ChemComp-U42 / [( #11: Chemical | ChemComp-U4Z / #14: Chemical | ChemComp-HEC / #15: Chemical | ChemComp-CA / | #16: Chemical | ChemComp-PGV / ( #17: Chemical | ChemComp-UNL / Num. of mol.: 17 / Source method: obtained synthetically #18: Chemical | #19: Chemical | #20: Chemical | ChemComp-PEF / | #21: Chemical | ChemComp-MN / | #22: Chemical | ChemComp-LHG / | |
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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-#8 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Roseiflexus castenholzii (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: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k 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: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 639374 / Symmetry type: POINT | ||||||||||||||||||||||||
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