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Yorodumi- EMDB-37465: Photosynthetic LH1-RC complex from the purple sulfur bacterium Al... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37465 | |||||||||||||||||||||
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Title | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by sucrose density | |||||||||||||||||||||
Map data | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum | |||||||||||||||||||||
Sample |
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Keywords | 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 / electron transfer activity / iron ion binding / heme binding ...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 / electron transfer activity / iron ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Allochromatium vinosum DSM 180 (bacteria) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.24 Å | |||||||||||||||||||||
Authors | Tani K / Kanno R / Harada A / Kobayashi A / Minamino A / Nakamura N / Ji X-C / Purba ER / Hall M / Yu L-J ...Tani K / Kanno R / Harada A / Kobayashi A / Minamino A / Nakamura N / Ji X-C / Purba ER / Hall M / Yu L-J / Madigan MT / Mizoguchi A / Iwasaki K / Humbel BM / Kimura Y / Wang-Otomo Z-Y | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Commun Biol / Year: 2024 Title: High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum. Authors: Kazutoshi Tani / Ryo Kanno / Ayaka Harada / Yuki Kobayashi / Akane Minamino / Shinji Takenaka / Natsuki Nakamura / Xuan-Cheng Ji / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael ...Authors: Kazutoshi Tani / Ryo Kanno / Ayaka Harada / Yuki Kobayashi / Akane Minamino / Shinji Takenaka / Natsuki Nakamura / Xuan-Cheng Ji / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Kenji Iwasaki / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo / Abstract: The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur ...The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur metabolism, and its core light-harvesting (LH1) complex has been a focus of numerous studies of photosynthetic light reactions. However, despite intense efforts, no high-resolution structure and thorough biochemical analysis of the Alc. vinosum LH1 complex have been reported. Here we present cryo-EM structures of the Alc. vinosum LH1 complex associated with reaction center (RC) at 2.24 Å resolution. The overall structure of the Alc. vinosum LH1 resembles that of its moderately thermophilic relative Alc. tepidum in that it contains multiple pigment-binding α- and β-polypeptides. Unexpectedly, however, six Ca ions were identified in the Alc. vinosum LH1 bound to certain α1/β1- or α1/β3-polypeptides through a different Ca-binding motif from that seen in Alc. tepidum and other Chromatiaceae that contain Ca-bound LH1 complexes. Two water molecules were identified as additional Ca-coordinating ligands. Based on these results, we reexamined biochemical and spectroscopic properties of the Alc. vinosum LH1-RC. While modest but distinct effects of Ca were detected in the absorption spectrum of the Alc. vinosum LH1 complex, a marked decrease in thermostability of its LH1-RC complex was observed upon removal of Ca. The presence of Ca in the photocomplex of Alc. vinosum suggests that Ca-binding to LH1 complexes may be a common adaptation in species of Chromatiaceae for conferring spectral and thermal flexibility on this key component of their photosynthetic machinery. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37465.map.gz | 394.5 MB | EMDB map data format | |
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Header (meta data) | emd-37465-v30.xml emd-37465.xml | 32.1 KB 32.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37465_fsc.xml | 16.4 KB | Display | FSC data file |
Images | emd_37465.png | 99.8 KB | ||
Filedesc metadata | emd-37465.cif.gz | 8.3 KB | ||
Others | emd_37465_half_map_1.map.gz emd_37465_half_map_2.map.gz | 339 MB 338.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37465 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37465 | HTTPS FTP |
-Related structure data
Related structure data | 8wduMC 8wdvC 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_37465.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Photosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.606 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Odd half map
File | emd_37465_half_map_1.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Even half map
File | emd_37465_half_map_2.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Photosynthetic LH1-RC complex from the purple sulfur phototrophic...
+Supramolecule #1: Photosynthetic LH1-RC complex from the purple sulfur phototrophic...
+Macromolecule #1: Photosynthetic reaction center cytochrome c subunit
+Macromolecule #2: Reaction center protein L chain
+Macromolecule #3: Reaction center protein M chain
+Macromolecule #4: Photosynthetic reaction center H subunit
+Macromolecule #5: Antenna complex alpha/beta subunit
+Macromolecule #6: Antenna complex alpha/beta subunit
+Macromolecule #7: Antenna complex alpha/beta subunit
+Macromolecule #8: Antenna complex alpha/beta subunit
+Macromolecule #9: Antenna complex alpha/beta subunit
+Macromolecule #10: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
+Macromolecule #13: PALMITIC ACID
+Macromolecule #14: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #15: BACTERIOCHLOROPHYLL A
+Macromolecule #16: BACTERIOPHEOPHYTIN A
+Macromolecule #17: Ubiquinone-8
+Macromolecule #18: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #19: CARDIOLIPIN
+Macromolecule #20: FE (III) ION
+Macromolecule #21: MENAQUINONE 8
+Macromolecule #22: SPIRILLOXANTHIN
+Macromolecule #23: CALCIUM ION
+Macromolecule #24: LAURYL DIMETHYLAMINE-N-OXIDE
+Macromolecule #25: 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: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 44 / Target criteria: Correlation coefficient |
Output model | PDB-8wdu: |