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Yorodumi- EMDB-16759: Cryo-EM structure of retinal-free proteoopsin bound to decanoate -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16759 | |||||||||
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Title | Cryo-EM structure of retinal-free proteoopsin bound to decanoate | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Membrane protein / Light-driven proton pump / Proteorhodopsin / Proteoopsin / PROTON TRANSPORT | |||||||||
Function / homology | Function and homology information light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / plasma membrane Similarity search - Function | |||||||||
Biological species | uncultured Gammaproteobacteria bacterium (environmental samples) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Hirschi S / Lemmin T / Fotiadis D | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: To Be Published Title: Structural insights into proteorhodopsin biogenesis and retinal scavenging Authors: Hirschi S / Lemmin T / Ayoub N / Kalbermatter D / Pellegata D / Ucurum Z / Gertsch J / Fotiadis D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16759.map.gz | 20.3 MB | EMDB map data format | |
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Header (meta data) | emd-16759-v30.xml emd-16759.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_16759.png | 166.1 KB | ||
Filedesc metadata | emd-16759.cif.gz | 5.2 KB | ||
Others | emd_16759_half_map_1.map.gz emd_16759_half_map_2.map.gz | 20.9 MB 20.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16759 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16759 | HTTPS FTP |
-Related structure data
Related structure data | 8cnkMC 8cqcC 8cqdC 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_16759.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.99231 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_16759_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16759_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pentameric proteoopsin bound to decanoate
Entire | Name: Pentameric proteoopsin bound to decanoate |
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Components |
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-Supramolecule #1: Pentameric proteoopsin bound to decanoate
Supramolecule | Name: Pentameric proteoopsin bound to decanoate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: uncultured Gammaproteobacteria bacterium (environmental samples) |
-Macromolecule #1: Green-light absorbing proteorhodopsin
Macromolecule | Name: Green-light absorbing proteorhodopsin / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: uncultured Gammaproteobacteria bacterium (environmental samples) |
Molecular weight | Theoretical: 26.359627 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAGGGDLDAS DYTGVSFWLV TAALLASTVF FFVERDRVSA KWKTSLTVSG LVTGIAFWHY MYMRGVWIET GDSPTVFRYI DWLLTVPLL ICEFYLILAA ATNVAGSLFK KLLVGSLVML VFGYMGEAGI MAAWPAFIIG CLAWVYMIYE LWAGEGKSAC N TASPAVQS ...String: MAGGGDLDAS DYTGVSFWLV TAALLASTVF FFVERDRVSA KWKTSLTVSG LVTGIAFWHY MYMRGVWIET GDSPTVFRYI DWLLTVPLL ICEFYLILAA ATNVAGSLFK KLLVGSLVML VFGYMGEAGI MAAWPAFIIG CLAWVYMIYE LWAGEGKSAC N TASPAVQS AYNTMMYIII FGWAIYPVGY FTGYLMGDGG SALNLNLIYN LADFVNKILF GLIIWNVAVK ESSNAGHHHH H UniProtKB: Green-light absorbing proteorhodopsin |
-Macromolecule #2: DECANOIC ACID
Macromolecule | Name: DECANOIC ACID / type: ligand / ID: 2 / Number of copies: 5 / Formula: DKA |
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Molecular weight | Theoretical: 172.265 Da |
Chemical component information | ChemComp-DKA: |
-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: 7.5 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 947286 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |