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Yorodumi- EMDB-13441: Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY mon... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13441 | ||||||||||||
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Title | Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A | ||||||||||||
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Sample |
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Keywords | Photosynthetic bacteria / light harvesting complex / Cryo-EM / RC-LH1 / RC-LH1-PufX / RC-LH1-PufX-Y / 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 / photosynthesis / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Cereibacter sphaeroides 2.4.1 (bacteria) / Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (bacteria) / Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||
Authors | Qian P / Hunter CN | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Biochem J / Year: 2021 Title: Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5 Å. Authors: Pu Qian / David J K Swainsbury / Tristan I Croll / Jack H Salisbury / Elizabeth C Martin / Philip J Jackson / Andrew Hitchcock / Pablo Castro-Hartmann / Kasim Sader / C Neil Hunter / Abstract: Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed ...Reaction centre light-harvesting 1 (RC-LH1) complexes are the essential components of bacterial photosynthesis. The membrane-intrinsic LH1 complex absorbs light and the energy migrates to an enclosed RC where a succession of electron and proton transfers conserves the energy as a quinol, which is exported to the cytochrome bc1 complex. In some RC-LH1 variants quinols can diffuse through small pores in a fully circular, 16-subunit LH1 ring, while in others missing LH1 subunits create a gap for quinol export. We used cryogenic electron microscopy to obtain a 2.5 Å resolution structure of one such RC-LH1, a monomeric complex from Rhodobacter sphaeroides. The structure shows that the RC is partly enclosed by a 14-subunit LH1 ring in which each αβ heterodimer binds two bacteriochlorophylls and, unusually for currently reported complexes, two carotenoids rather than one. Although the extra carotenoids confer an advantage in terms of photoprotection and light harvesting, they could impede passage of quinones through small, transient pores in the LH1 ring, necessitating a mechanism to create a dedicated quinone channel. The structure shows that two transmembrane proteins play a part in stabilising an open ring structure; one of these components, the PufX polypeptide, is augmented by a hitherto undescribed protein subunit we designate as protein-Y, which lies against the transmembrane regions of the thirteenth and fourteenth LH1α polypeptides. Protein-Y prevents LH1 subunits 11-14 adjacent to the RC QB site from bending inwards towards the RC and, with PufX preventing complete encirclement of the RC, this pair of polypeptides ensures unhindered quinone diffusion. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: qian P / Hunter CN #2: Journal: To Be Published Title: Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A Authors: Qian P / Hunter CN | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13441.map.gz | 37.1 MB | EMDB map data format | |
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Header (meta data) | emd-13441-v30.xml emd-13441.xml | 25.2 KB 25.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13441_fsc.xml | 18.2 KB | Display | FSC data file |
Images | emd_13441.png | 108.3 KB | ||
Filedesc metadata | emd-13441.cif.gz | 7.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13441 | HTTPS FTP |
-Validation report
Summary document | emd_13441_validation.pdf.gz | 413.4 KB | Display | EMDB validaton report |
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Full document | emd_13441_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | emd_13441_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_13441_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13441 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13441 | HTTPS FTP |
-Related structure data
Related structure data | 7pilMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13441.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Light harvesting complex
+Supramolecule #1: Light harvesting complex
+Macromolecule #1: Light-harvesting protein B-875 alpha chain
+Macromolecule #2: Light-harvesting protein B-875 beta chain
+Macromolecule #3: Reaction center protein H chain
+Macromolecule #4: Reaction center protein L chain
+Macromolecule #5: Reaction center protein M chain
+Macromolecule #6: RC-Y
+Macromolecule #7: Intrinsic membrane protein PufX
+Macromolecule #8: BACTERIOCHLOROPHYLL A
+Macromolecule #9: SPHEROIDENE
+Macromolecule #10: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #11: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #12: BACTERIOPHEOPHYTIN A
+Macromolecule #13: UBIQUINONE-10
+Macromolecule #14: UBIQUINONE-1
+Macromolecule #15: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...
+Macromolecule #16: FE (III) ION
+Macromolecule #17: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.0 mg/mL |
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Buffer | pH: 7.8 / Component - Concentration: 20.0 mMol / Component - Formula: HEPES / Details: 20 mM HEPES, pH 7.8 , 0.03% beta-DDM |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: QF R1.2/1.3 grid coated graphene oxide. |
Details | in 0.03% beta-DDM detergent |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3180 / Average exposure time: 12.21 sec. / Average electron dose: 44.94 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |