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Yorodumi- PDB-5yq7: Cryo-EM structure of the RC-LH core complex from Roseiflexus cast... -
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-Basic information
Entry | Database: PDB / ID: 5yq7 | |||||||||
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Title | Cryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Photosynthetic core complex | |||||||||
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: 4.1 Å | |||||||||
Authors | Shi, Y. / Xin, Y.Y. / Niu, T.X. / Wang, Q.Q. / Niu, W.Q. / Huang, X.J. / Ding, W. / Blankenship, R.E. / Xu, X.L. / Sun, F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Cryo-EM structure of the RC-LH core complex from an early branching photosynthetic prokaryote. Authors: Yueyong Xin / Yang Shi / Tongxin Niu / Qingqiang Wang / Wanqiang Niu / Xiaojun Huang / Wei Ding / Lei Yang / Robert E Blankenship / Xiaoling Xu / Fei Sun / Abstract: Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important ...Photosynthetic prokaryotes evolved diverse light-harvesting (LH) antennas to absorb sunlight and transfer energy to reaction centers (RC). The filamentous anoxygenic phototrophs (FAPs) are important early branching photosynthetic bacteria in understanding the origin and evolution of photosynthesis. How their photosynthetic machinery assembles for efficient energy transfer is yet to be elucidated. Here, we report the 4.1 Å structure of photosynthetic core complex from Roseiflexus castenholzii by cryo-electron microscopy. The RC-LH complex has a tetra-heme cytochrome c bound RC encompassed by an elliptical LH ring that is assembled from 15 LHαβ subunits. An N-terminal transmembrane helix of cytochrome c inserts into the LH ring, not only yielding a tightly bound cytochrome c for rapid electron transfer, but also opening a slit in the LH ring, which is further flanked by a transmembrane helix from a newly discovered subunit X. These structural features suggest an unusual quinone exchange model of prokaryotic photosynthetic machinery. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5yq7.cif.gz | 457.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yq7.ent.gz | 403.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yq7_validation.pdf.gz | 3.7 MB | Display | wwPDB validaton report |
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Full document | 5yq7_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 5yq7_validation.xml.gz | 96.3 KB | Display | |
Data in CIF | 5yq7_validation.cif.gz | 126.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/5yq7 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/5yq7 | HTTPS FTP |
-Related structure data
Related structure data | 6828MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 16 molecules EB08642KIGWUSQOC
#1: Protein | Mass: 6431.528 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD2 #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 |
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-Precursor for ... , 2 types, 2 molecules LM
#2: Protein | Mass: 34432.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD0 |
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#7: Protein | Mass: 34948.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD0 |
-Protein/peptide , 3 types, 17 molecules TVRPNJHFDA97531YX
#4: 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: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The peptide could be either an unidentified new gene product or a proteolytic fragment of the pufLM gene product that is cleaved twice during processing. Source: (natural) Roseiflexus castenholzii (bacteria) #6: Protein/peptide | | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Subunit X with its flexible transmembrane helix is flanking the gap of light harvesting complex. Source: (natural) Roseiflexus castenholzii (bacteria) |
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-Non-polymers , 6 types, 72 molecules
#8: Chemical | ChemComp-BCL / #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-FE / | #12: Chemical | ChemComp-HEM / #13: Chemical | ChemComp-KGD / |
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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: Photosynthetic core complex / Type: COMPLEX / Entity ID: #1-#2, #7, #3-#5 / Source: NATURAL |
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Molecular weight | Value: 0.33 MDa / Experimental value: NO |
Source (natural) | Organism: Roseiflexus castenholzii (bacteria) |
Buffer solution | pH: 8.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 50 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2330 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 148618 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256903 / Symmetry type: POINT | ||||||||||||||||||||||||
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