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- PDB-8hju: Cryo-EM structure of native RC-LH complex from Roseiflexus casten... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hju | ||||||
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Title | Cryo-EM structure of native RC-LH complex from Roseiflexus castenholzii at 10,000 lux | ||||||
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![]() | PHOTOSYNTHESIS / RC-LH core complex | ||||||
Function / homology | ![]() organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / chlorophyll 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 light-harvesting complex / bacteriochlorophyll binding / chlorophyll 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 | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Xu, X. / Xin, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Carotenoid assembly regulates quinone diffusion and the reaction center-light harvesting complex architecture. Authors: Jiyu Xin / Yang Shi / Xin Zhang / Xinyi Yuan / Yueyong Xin / Huimin He / Jiejie Shen / Robert E Blankenship / Xiaoling Xu / ![]() ![]() Abstract: Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships ...Carotenoid (Car) pigments perform central roles in photosynthesis-related light harvesting (LH), photoprotection, and assembly of functional pigment-protein complexes. However, the relationships between Car depletion in the LH, assembly of the prokaryotic reaction center (RC)-LH complex, and quinone exchange are not fully understood. Here, we analyzed native RC-LH (nRC-LH) and Car-depleted RC-LH (dRC-LH) complexes in , a chlorosome-less filamentous anoxygenic phototroph that forms the deepest branch of photosynthetic bacteria. Newly identified exterior Cars functioned with the bacteriochlorophyll B800 to block the proposed quinone channel between LHαβ subunits in the nRC-LH, forming a sealed LH ring that was disrupted by transmembrane helices from cytochrome and subunit X to allow quinone shuttling. dRC-LH lacked subunit X, leading to an exposed LH ring with a larger opening, which together accelerated the quinone exchange rate. We also assigned amino acid sequences of subunit X and two hypothetical proteins Y and Z that functioned in forming the quinone channel and stabilizing the RC-LH interactions. This study reveals the structural basis by which Cars assembly regulates the architecture and quinone exchange of bacterial RC-LH complexes. These findings mark an important step forward in understanding the evolution and diversity of prokaryotic photosynthetic apparatus. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 521.7 KB | Display | ![]() |
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PDB format | ![]() | 456.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.1 MB | Display | ![]() |
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Full document | ![]() | 5.5 MB | Display | |
Data in XML | ![]() | 145.3 KB | Display | |
Data in CIF | ![]() | 161.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34838MC ![]() 8hjvC ![]() 8j5oC ![]() 8j5pC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 3 types, 17 molecules 02468BEGIKOQSUWCZ
#1: Protein | Mass: 6431.528 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q83XD2 #5: Protein | | Mass: 34923.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: A7NQE7 #8: Protein | | Mass: 6927.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBI:WP_041331144.1 Source: (natural) ![]() |
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-Protein/peptide , 3 types, 17 molecules 13579ADFHJNPRTVXY
#2: Protein/peptide | Mass: 4724.656 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q83XD1 #6: Protein/peptide | | Mass: 3628.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CDS 1,089,486-1,089,602 Source: (natural) ![]() #7: Protein/peptide | | Mass: 4493.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CDS 1,060,366-1,060,464 Source: (natural) ![]() |
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-Reaction center protein ... , 2 types, 2 molecules LM
#3: Protein | Mass: 34844.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE L- AND M-SUBUNITS OF THE RC ARE ENCODED BY A FUSED GENE PUFLM BUT POST-TRANSLATIONAL PROCESSED INTO TWO DISCRETE SUBUNITS EACH CONTAINING SIX AND FIVE TRANSMEMBRANE HELICES Source: (natural) ![]() References: UniProt: A7NQE8 |
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#4: Protein | Mass: 35046.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: THE L- AND M-SUBUNITS OF THE RC ARE ENCODED BY A FUSED GENE PUFLM BUT POST-TRANSLATIONAL PROCESSED INTO TWO DISCRETE SUBUNITS EACH CONTAINING SIX AND FIVE TRANSMEMBRANE HELICES Source: (natural) ![]() References: UniProt: A7NQE8 |
-Non-polymers , 8 types, 97 molecules ![](data/chem/img/BCL.gif)
![](data/chem/img/KGD.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/MQE.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/DGA.gif)
![](data/chem/img/KGD.gif)
![](data/chem/img/BPH.gif)
![](data/chem/img/MQE.gif)
![](data/chem/img/PGV.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/DGA.gif)
#9: Chemical | ChemComp-BCL / #10: Chemical | ChemComp-KGD / #11: Chemical | #12: Chemical | #13: Chemical | ChemComp-PGV / ( #14: Chemical | ChemComp-FE / | #15: Chemical | ChemComp-HEM / #16: Chemical | ChemComp-DGA / | |
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-Details
Has ligand of interest | N |
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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 |
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Sample preparation
Component | Name: THE NATIVE RC-LH COMPLEX / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||||||||||||||
Electron gun | Electron source: ![]() | ||||||||||||||||||||||||
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm | ||||||||||||||||||||||||
Image recording |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372029 / Symmetry type: POINT |
Refinement | Highest resolution: 2.8 Å |