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- EMDB-32192: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER S... -
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Open data
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Basic information
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Title | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES DIMER | |||||||||||||||||||||
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Function / homology | ![]() 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 / membrane => GO:0016020 / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||||||||||||||
![]() | Tani K / Kanno R / Kawamura S / Kikuchi R / Nagashima KVP / Hall M / Takahashi A / Yu L-J / Kimura Y / Madigan MT ...Tani K / Kanno R / Kawamura S / Kikuchi R / Nagashima KVP / Hall M / Takahashi A / Yu L-J / Kimura Y / Madigan MT / Mizoguchi A / Humbel BM / Wang-Otomo Z-Y | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex. Authors: Kazutoshi Tani / Ryo Kanno / Riku Kikuchi / Saki Kawamura / Kenji V P Nagashima / Malgorzata Hall / Ai Takahashi / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / ...Authors: Kazutoshi Tani / Ryo Kanno / Riku Kikuchi / Saki Kawamura / Kenji V P Nagashima / Malgorzata Hall / Ai Takahashi / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo / ![]() ![]() ![]() Abstract: Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM ...Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 β-polypeptides, indicating a critical role for protein-U in controlling the number of αβ-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex. | |||||||||||||||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 325.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.3 KB 24.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 108.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vy2MC ![]() 7vy3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
+Entire : Photosynthetic LH1-RC complex from the purple phototrophic bacter...
+Supramolecule #1: Photosynthetic LH1-RC complex from the purple phototrophic bacter...
+Supramolecule #2: Rhodobacter sphaeroides Dimeric LH1-RC Complex
+Macromolecule #1: Photosynthetic reaction center L subunit
+Macromolecule #2: Reaction center protein M chain
+Macromolecule #3: Photosynthetic reaction center subunit H
+Macromolecule #4: Antenna pigment protein alpha chain
+Macromolecule #5: Antenna pigment protein beta chain
+Macromolecule #6: PufX
+Macromolecule #7: protein-U
+Macromolecule #8: BACTERIOCHLOROPHYLL A
+Macromolecule #9: BACTERIOPHEOPHYTIN A
+Macromolecule #10: UBIQUINONE-10
+Macromolecule #11: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #12: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #13: FE (III) ION
+Macromolecule #14: SPHEROIDENE
+Macromolecule #15: CARDIOLIPIN
+Macromolecule #16: PHOSPHATIDYLETHANOLAMINE
+Macromolecule #17: LAURYL DIMETHYLAMINE-N-OXIDE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.0 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
Details | This sample was monodisperse. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.275 sec. / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |