+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3951 | |||||||||
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Title | Reaction centre light harvesting complex 1 from Blc. virids | |||||||||
Map data | Cryo-EM images of Reaction centre-light harvesting complex 1 (RC-LH1) from Blc. viridis were processed using RELION 2.0. The 3D cryo-EM map was produced after Post-processing to 2.87 Angstrom. | |||||||||
Sample |
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Function / homology | Function and homology information light-harvesting complex / 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 ...light-harvesting complex / 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 => GO:0016020 / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Blastochloris viridis (bacteria) / Rhodopseudomonas viridis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Qian P / Siebert CA / Canniffe DP / Wang P / Hunter CN | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM structure of the Blastochloris viridis LH1-RC complex at 2.9 Å. Authors: Pu Qian / C Alistair Siebert / Peiyi Wang / Daniel P Canniffe / C Neil Hunter / Abstract: The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the ...The light-harvesting 1-reaction centre (LH1-RC) complex is a key functional component of bacterial photosynthesis. Here we present a 2.9 Å resolution cryo-electron microscopy structure of the bacteriochlorophyll b-based LH1-RC complex from Blastochloris viridis that reveals the structural basis for absorption of infrared light and the molecular mechanism of quinone migration across the LH1 complex. The triple-ring LH1 complex comprises a circular array of 17 β-polypeptides sandwiched between 17 α- and 16 γ-polypeptides. Tight packing of the γ-apoproteins between β-polypeptides collectively interlocks and stabilizes the LH1 structure; this, together with the short Mg-Mg distances of bacteriochlorophyll b pairs, contributes to the large redshift of bacteriochlorophyll b absorption. The 'missing' 17th γ-polypeptide creates a pore in the LH1 ring, and an adjacent binding pocket provides a folding template for a quinone, Q , which adopts a compact, export-ready conformation before passage through the pore and eventual diffusion to the cytochrome bc complex. | |||||||||
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_3951.map.gz | 35.8 MB | EMDB map data format | |
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Header (meta data) | emd-3951-v30.xml emd-3951.xml | 28.1 KB 28.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3951_fsc.xml | 8.2 KB | Display | FSC data file |
Images | emd_3951.png | 175.6 KB | ||
Others | emd_3951_half_map_1.map.gz emd_3951_half_map_2.map.gz | 22.2 MB 22.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3951 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3951 | HTTPS FTP |
-Related structure data
Related structure data | 6et5MC 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_3951.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM images of Reaction centre-light harvesting complex 1 (RC-LH1) from Blc. viridis were processed using RELION 2.0. The 3D cryo-EM map was produced after Post-processing to 2.87 Angstrom. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: First half of map from last round of calculation Refine3D in RELION.
File | emd_3951_half_map_1.map | ||||||||||||
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Annotation | First half of map from last round of calculation Refine3D in RELION. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half of map from last round of calculation Refine3D in RELION.
File | emd_3951_half_map_2.map | ||||||||||||
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Annotation | Second half of map from last round of calculation Refine3D in RELION. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Reaction centre-Light harvesting complex 1 (RC-LH1)
+Supramolecule #1: Reaction centre-Light harvesting complex 1 (RC-LH1)
+Macromolecule #1: Photosynthetic reaction center cytochrome c subunit
+Macromolecule #2: Reaction center protein L chain
+Macromolecule #3: Reaction center protein M chain
+Macromolecule #4: Reaction center protein H chain
+Macromolecule #5: Light-harvesting protein B-1015 alpha chain
+Macromolecule #6: Light-harvesting protein B-1015 beta chain
+Macromolecule #7: Light-harvesting protein B-1015 gamma chain
+Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #9: BACTERIOCHLOROPHYLL B
+Macromolecule #10: BACTERIOPHEOPHYTIN B
+Macromolecule #11: Ubiquinone-9
+Macromolecule #12: FE (III) ION
+Macromolecule #13: SULFATE ION
+Macromolecule #14: LAURYL DIMETHYLAMINE-N-OXIDE
+Macromolecule #15: MENAQUINONE-9
+Macromolecule #16: 15-cis-1,2-dihydroneurosporene
+Macromolecule #17: all-trans-1,2-dihydroneurosporene
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Concentration | 4.0 mg/mL |
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Buffer | pH: 7.8 / Component - Concentration: 20.0 mMol / Component - Name: HEPES / Details: 20 mMol HEPES, pH 7.8, 100 mM NaCl |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0002 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 278 K / Instrument: LEICA EM GP Details: Blot for 3.5 seconds. Humidity: 99% Temperature:4C.. |
Details | Protein was solubilised by the use detergent of beta-DDM. The protein particle therefore contains a detergent belt in its hydrophobic region. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number grids imaged: 3 / Number real images: 6472 / Average exposure time: 0.5 sec. / Average electron dose: 2.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE |
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Output model | PDB-6et5: |