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- EMDB-53519: Cryo-EM structure of the flotillin-associated rhodopsin PsFAR in ... -
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Open data
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Basic information
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Title | Cryo-EM structure of the flotillin-associated rhodopsin PsFAR in detergent micelle | ||||||||||||
![]() | Sharpened map used for manual and automatic structure refinement | ||||||||||||
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![]() | flotillin / rhodopsin / retinal / MEMBRANE PROTEIN | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.56 Å | ||||||||||||
![]() | Kovalev K / Stetsenko A / Marin E / Guskov A | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis for no retinal binding in flotillin-associated rhodopsins. Authors: Kirill Kovalev / Artem Stetsenko / Florian Trunk / Egor Marin / Jose M Haro-Moreno / Gerrit H U Lamm / Alexey Alekseev / Francisco Rodriguez-Valera / Thomas R Schneider / Josef Wachtveitl / Albert Guskov / ![]() ![]() ![]() Abstract: Rhodopsins are light-sensitive membrane proteins capturing solar energy via a retinal cofactor covalently attached to a lysine residue. Several groups of rhodopsins lack the conserved lysine and ...Rhodopsins are light-sensitive membrane proteins capturing solar energy via a retinal cofactor covalently attached to a lysine residue. Several groups of rhodopsins lack the conserved lysine and showed no retinal binding. Recently, flotillin-associated rhodopsins (FArhodopsins or FARs) were identified and suggested to lack the retinal-binding pocket despite preserving the lysine residue in many members of the group. Here, we present cryoelectron microscopic (cryo-EM) structures of paralog FArhodopsin and proteorhodopsin from marine bacterium Pseudothioglobus, both forming pentamers similar to those of other microbial rhodopsins. We demonstrate no binding of retinal to the FArhodopsin despite preservation of the lysine residue and overall similarity of the protein fold and internal organization to those of the retinal-binding paralog. Mutational analysis confirmed that two amino acids, H84 and E120, prevent retinal binding within the FArhodopsin. Our work provides insights into the natural retinal loss in microbial rhodopsins and might contribute to the further understanding of FArhodopsins. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 203.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.9 KB 17.9 KB | Display Display | ![]() |
Images | ![]() | 77.7 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() | 107.5 MB 200.7 MB 200.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 826.3 KB | Display | ![]() |
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Full document | ![]() | 825.9 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9r21MC ![]() 9r22C ![]() 9r23C M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Sharpened map used for manual and automatic structure refinement | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.836 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Volume map used for validation against coordinates
File | emd_53519_additional_1.map | ||||||||||||
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Annotation | Volume map used for validation against coordinates | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_53519_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_53519_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : flotillin-associated rhodopsin PsFAR
Entire | Name: flotillin-associated rhodopsin PsFAR |
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Components |
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-Supramolecule #1: flotillin-associated rhodopsin PsFAR
Supramolecule | Name: flotillin-associated rhodopsin PsFAR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: pentamer of the protein in detergent micelle |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 135 KDa |
-Macromolecule #1: flotillin-associated rhodopsin
Macromolecule | Name: flotillin-associated rhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 27.518244 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNSTLLPTDI VGGTFWLLSM ALIGASIFFL LERNRVDGRW HTTMTLLGVT MLISAIFYYY VQGMWVDTGK APIVLRYLDW ILTHSMQVV MFYVILTAVT KVSSALFWRL LIGALVMVIG EFLGAAGYMS ATLGFIIGVV GWLYILGEIY MGEASRCNIE S GNEATHMA ...String: MNSTLLPTDI VGGTFWLLSM ALIGASIFFL LERNRVDGRW HTTMTLLGVT MLISAIFYYY VQGMWVDTGK APIVLRYLDW ILTHSMQVV MFYVILTAVT KVSSALFWRL LIGALVMVIG EFLGAAGYMS ATLGFIIGVV GWLYILGEIY MGEASRCNIE S GNEATHMA FNGLRLILTI GWAIYPLGYF INNLGGGVDA NSLNIIYNLT DFLNKIIFGF VVYRAAMNDT QARLDEIKKL EH HHHHH |
-Macromolecule #2: EICOSANE
Macromolecule | Name: EICOSANE / type: ligand / ID: 2 / Number of copies: 81 / Formula: LFA |
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Molecular weight | Theoretical: 282.547 Da |
Chemical component information | ![]() ChemComp-LFA: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 97 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting 4-6 second, force 0. |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |