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- EMDB-12680: Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimo... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12680 | ||||||||||||||||||||||||
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Title | Cryo-EM structure (model_2a) of the RC-dLH complex from Gemmatimonas phototrophica at 2.5 A | ||||||||||||||||||||||||
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Function / homology | ![]() organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / chlorophyll 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 light-harvesting complex / bacteriochlorophyll binding / chlorophyll 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 | ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||||||||||||||
![]() | Qian P / Koblizek M | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: 2.4-Å structure of the double-ring photosystem. Authors: Pu Qian / Alastair T Gardiner / Ivana Šímová / Katerina Naydenova / Tristan I Croll / Philip J Jackson / Nupur / Miroslav Kloz / Petra Čubáková / Marek Kuzma / Yonghui Zeng / Pablo ...Authors: Pu Qian / Alastair T Gardiner / Ivana Šímová / Katerina Naydenova / Tristan I Croll / Philip J Jackson / Nupur / Miroslav Kloz / Petra Čubáková / Marek Kuzma / Yonghui Zeng / Pablo Castro-Hartmann / Bart van Knippenberg / Kenneth N Goldie / David Kaftan / Pavel Hrouzek / Jan Hájek / Jon Agirre / C Alistair Siebert / David Bína / Kasim Sader / Henning Stahlberg / Roman Sobotka / Christopher J Russo / Tomáš Polívka / C Neil Hunter / Michal Koblížek / ![]() ![]() ![]() ![]() Abstract: Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo- ...Phototrophic Gemmatimonadetes evolved the ability to use solar energy following horizontal transfer of photosynthesis-related genes from an ancient phototrophic proteobacterium. The electron cryo-microscopy structure of the photosystem at 2.4 Å reveals a unique, double-ring complex. Two unique membrane-extrinsic polypeptides, RC-S and RC-U, hold the central type 2 reaction center (RC) within an inner 16-subunit light-harvesting 1 (LH1) ring, which is encircled by an outer 24-subunit antenna ring (LHh) that adds light-gathering capacity. Femtosecond kinetics reveal the flow of energy within the RC-dLH complex, from the outer LHh ring to LH1 and then to the RC. This structural and functional study shows that has independently evolved its own compact, robust, and highly effective architecture for harvesting and trapping solar energy. | ||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 18.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 33.8 KB 33.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.1 KB | Display | ![]() |
Images | ![]() | 75.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 345.3 KB | Display | ![]() |
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Full document | ![]() | 344.9 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o0vMC ![]() 7o0uC ![]() 7o0wC ![]() 7o0xC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 12.1 TB Data #1: Unaligned multi-frame micrographs of RC-dLH1 complexes on HexAuFoil support [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.99946 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : RC-dLH (model_2a)
+Supramolecule #1: RC-dLH (model_2a)
+Macromolecule #1: LHh-alpha
+Macromolecule #2: LHh-alpha
+Macromolecule #3: Light-harvesting protein B:885 subunit beta
+Macromolecule #4: Light-harvesting protein B:885 subunit beta
+Macromolecule #5: MULTIHEME_CYTC domain-containing protein
+Macromolecule #6: RC-S
+Macromolecule #7: PRCH domain-containing protein
+Macromolecule #8: RC-Hc
+Macromolecule #9: Photosynthetic reaction center L subunit
+Macromolecule #10: RC-M
+Macromolecule #11: LHC domain-containing protein
+Macromolecule #12: LHC domain-containing protein
+Macromolecule #14: BACTERIOCHLOROPHYLL A
+Macromolecule #15: DODECYL-BETA-D-MALTOSIDE
+Macromolecule #16: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...
+Macromolecule #17: HEME C
+Macromolecule #18: (2~{S},3~{S},4~{S},5~{S})-4,5-diacetyloxy-3-oxidanyl-oxane-2-carb...
+Macromolecule #19: 2-acetamido-2-deoxy-alpha-D-glucopyranose
+Macromolecule #20: (19R,22S)-25-amino-22-hydroxy-22-oxido-16-oxo-17,21,23-trioxa-22l...
+Macromolecule #21: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...
+Macromolecule #22: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...
+Macromolecule #23: MENAQUINONE 8
+Macromolecule #24: [(2~{S})-3-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[...
+Macromolecule #25: BACTERIOPHEOPHYTIN A
+Macromolecule #26: FE (III) ION
+Macromolecule #27: SPIRILLOXANTHIN
+Macromolecule #28: [(2~{S})-3-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4...
+Macromolecule #29: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 6.5 mg/mL | ||||||
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Buffer | pH: 8 / Component:
Details: The final purified complex is in 20mM Tris.Cl, 0.025 DDM, PH 8.0 buffer. | ||||||
Grid | Model: Homemade / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 30.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Talmon type. | ||||||
Details | The protein complex was isolated from photosynthetic membrane using detergent beta-DDM. After purification, concentrated protein sample solution was stored in LN before using. |
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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: 19865 / Average exposure time: 1.2 sec. / Average electron dose: 24.8 e/Å2 Details: All movies were recorded from a HexAuFoil grid with a special EPU version, which can recognise 300 nm holes on the grid. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.4 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 |