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Open data
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Basic information
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Title | FAD_AQ bound blue-light state structure of PdLCry | |||||||||||||||
![]() | FAD_ASQ bound blue-light state structure of PdLCry - lowpass filtered to 8 Angstrom | |||||||||||||||
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![]() | light-sensitive / circalunar clock / FLAVOPROTEIN | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||||||||
![]() | Behrmann E / Behrmann H | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A marine cryptochrome with an inverse photo-oligomerization mechanism. Authors: Hong Ha Vu / Heide Behrmann / Maja Hanić / Gayathri Jeyasankar / Shruthi Krishnan / Dennis Dannecker / Constantin Hammer / Monika Gunkel / Ilia A Solov'yov / Eva Wolf / Elmar Behrmann / ![]() Abstract: Cryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle worm Platynereis dumerilii, ...Cryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle worm Platynereis dumerilii, its light receptive cryptochrome L-CRY (PdLCry) allows the animal to discriminate between sunlight and moonlight, an important requirement for synchronizing its lunar cycle-dependent mass spawning. Using cryo-electron microscopy, we show that in the dark, PdLCry adopts a dimer arrangement observed neither in plant nor insect CRYs. Intense illumination disassembles the dimer into monomers. Structural and functional data suggest a mechanistic coupling between the light-sensing flavin adenine dinucleotide chromophore, the dimer interface, and the C-terminal tail helix, with a likely involvement of the phosphate binding loop. Taken together, our work establishes PdLCry as a CRY protein with inverse photo-oligomerization with respect to plant CRYs, and provides molecular insights into how this protein might help discriminating the different light intensities associated with sunlight and moonlight. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 116.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.3 KB 20.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 43 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() ![]() | 117.9 MB 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 668.3 KB | Display | ![]() |
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Full document | ![]() | 667.9 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | FAD_ASQ bound blue-light state structure of PdLCry - lowpass filtered to 8 Angstrom | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.862 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: FAD ASQ bound blue-light state structure of PdLCry - unfiltered map
File | emd_17533_additional_1.map | ||||||||||||
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Annotation | FAD_ASQ bound blue-light state structure of PdLCry - unfiltered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17533_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17533_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : monomeric PdLCry in the blue-light state
Entire | Name: monomeric PdLCry in the blue-light state |
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Components |
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-Supramolecule #1: monomeric PdLCry in the blue-light state
Supramolecule | Name: monomeric PdLCry in the blue-light state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 65 KDa |
-Macromolecule #1: light receptive cryptochrome
Macromolecule | Name: light receptive cryptochrome / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKEKMSAWEV GNGIMEEKTD DWDNKEDNGK EHVSLHWFRH GLRLHDNPAL LKSLEGAKEF YALFIWDGEV AGTKLVSYP RMKFLLECLK DLDDSLKKHG GRLYVVKGPS DVVIKQLIEE WGVTRVTCEI DPEPIWQPRD K AVKDLCAT KGVKWFDYNS HLLWDPKAVC ...String: MKEKMSAWEV GNGIMEEKTD DWDNKEDNGK EHVSLHWFRH GLRLHDNPAL LKSLEGAKEF YALFIWDGEV AGTKLVSYP RMKFLLECLK DLDDSLKKHG GRLYVVKGPS DVVIKQLIEE WGVTRVTCEI DPEPIWQPRD K AVKDLCAT KGVKWFDYNS HLLWDPKAVC DANGGRPPHT YKLFCQVTDL LGKPETPHPD PDFSHVQMPV SD DFDDKFG LPTLKELGCE PECEEQEKPF NKWQGGETGA LELLETRLMI ERTAYKAGYI MPNQYIPDLV GPP RSMSPH LRFGALSIRK FYWDLHNNYA EVCGGEWLGA LTAQLVWREY FYCMSYGNPS FDKMEGNPIC LQIP WYKDE EALEKWKQGQ TGFPWIDACM RQLRYEGWMH HVGRHAVACF LTRGDLWISW VDGLEAFYKY MLDGD WSVC AGNWMWVSSS AFENCLQCPQ CFSPVLYGMR MDPTGEFTRR YVPQLKNMPL KYLFQPWKAP KEVQEK AGC VIGEDYPSPM VDHKEASSKC RRMMEDVKSI IKDPEVWHCT PSDTNEVRKF CWLPEHMTAD QPCLGDL PC IKY GENBANK: GENBANK: UUF95169 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV Details: grids were illuminated for 30 secs in the humidifier chamber of the freeze-plunger using a 455 nm blue-light LED (Thorlabs M455L4, operated at 1000 mA). To ensure optimal illumination, a ...Details: grids were illuminated for 30 secs in the humidifier chamber of the freeze-plunger using a 455 nm blue-light LED (Thorlabs M455L4, operated at 1000 mA). To ensure optimal illumination, a liquid-light guide (Thorlabs LLG03-4H) was used to bring the light source within 3 mm of the grid surface. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Software | Name: EPU |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2 / Details: see material+methods |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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