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Yorodumi- EMDB-33931: Structure of photosynthetic LH1-RC super-complex of Rhodobacter c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33931 | |||||||||||||||||||||
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Title | Structure of photosynthetic LH1-RC super-complex of Rhodobacter capsulatus | |||||||||||||||||||||
Map data | negative B-factor applied map | |||||||||||||||||||||
Sample |
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Function / homology | Function and homology information organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Rhodobacter capsulatus (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||||||||||||||
Authors | Tani K / Kanno R / Ji X-C / Satoh I / Kobayashi Y / Nagashima KVP / Hall M / Yu L-J / Kimura Y / Mizoguchi A ...Tani K / Kanno R / Ji X-C / Satoh I / Kobayashi Y / Nagashima KVP / Hall M / Yu L-J / Kimura Y / Mizoguchi A / Humbel BM / Madigan MT / Wang-Otomo Z-Y | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Rhodobacter capsulatus forms a compact crescent-shaped LH1-RC photocomplex. Authors: Kazutoshi Tani / Ryo Kanno / Xuan-Cheng Ji / Itsusei Satoh / Yuki Kobayashi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Akira Mizoguchi / Bruno M Humbel / Michael T Madigan / Zheng-Yu Wang-Otomo / Abstract: Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the ...Rhodobacter (Rba.) capsulatus has been a favored model for studies of all aspects of bacterial photosynthesis. This purple phototroph contains PufX, a polypeptide crucial for dimerization of the light-harvesting 1-reaction center (LH1-RC) complex, but lacks protein-U, a U-shaped polypeptide in the LH1-RC of its close relative Rba. sphaeroides. Here we present a cryo-EM structure of the Rba. capsulatus LH1-RC purified by DEAE chromatography. The crescent-shaped LH1-RC exhibits a compact structure containing only 10 LH1 αβ-subunits. Four αβ-subunits corresponding to those adjacent to protein-U in Rba. sphaeroides were absent. PufX in Rba. capsulatus exhibits a unique conformation in its N-terminus that self-associates with amino acids in its own transmembrane domain and interacts with nearby polypeptides, preventing it from interacting with proteins in other complexes and forming dimeric structures. These features are discussed in relation to the minimal requirements for the formation of LH1-RC monomers and dimers, the spectroscopic behavior of both the LH1 and RC, and the bioenergetics of energy transfer from LH1 to the RC. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33931.map.gz | 228.8 MB | EMDB map data format | |
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Header (meta data) | emd-33931-v30.xml emd-33931.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33931_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_33931.png | 149.3 KB | ||
Others | emd_33931_half_map_1.map.gz emd_33931_half_map_2.map.gz | 194.6 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33931 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33931 | HTTPS FTP |
-Related structure data
Related structure data | 7ymlMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33931.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | negative B-factor applied map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half odd map
File | emd_33931_half_map_1.map | ||||||||||||
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Annotation | Half odd map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half even map
File | emd_33931_half_map_2.map | ||||||||||||
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Annotation | Half even map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosynthetic LH1-RC complex from the purple phototrophic bacter...
+Supramolecule #1: Photosynthetic LH1-RC complex from the purple phototrophic bacter...
+Macromolecule #1: Reaction center protein L chain
+Macromolecule #2: Reaction center protein M chain
+Macromolecule #3: Photosynthetic reaction center H subunit
+Macromolecule #4: Light-harvesting protein B-870 alpha chain
+Macromolecule #5: Light-harvesting protein B-870 beta chain
+Macromolecule #6: Photosynthetic reaction center PufX protein
+Macromolecule #7: BACTERIOCHLOROPHYLL A
+Macromolecule #8: BACTERIOPHEOPHYTIN A
+Macromolecule #9: UBIQUINONE-10
+Macromolecule #10: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #11: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
+Macromolecule #12: LAURYL DIMETHYLAMINE-N-OXIDE
+Macromolecule #13: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #14: FE (III) ION
+Macromolecule #15: SPHEROIDENE
+Macromolecule #16: MYRISTIC ACID
+Macromolecule #17: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5.0 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 31.8 sec. / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |