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- EMDB-17533: FAD_AQ bound blue-light state structure of PdLCry -

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Basic information

Entry
Database: EMDB / ID: EMD-17533
TitleFAD_AQ bound blue-light state structure of PdLCry
Map dataFAD_ASQ bound blue-light state structure of PdLCry - lowpass filtered to 8 Angstrom
Sample
  • Complex: monomeric PdLCry in the blue-light state
    • Protein or peptide: light receptive cryptochrome
Keywordslight-sensitive / circalunar clock / FLAVOPROTEIN
Biological speciesPlatynereis dumerilii (Dumeril's clam worm)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsBehrmann E / Behrmann H
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
German Research Foundation (DFG)SFB1372 Germany
German Research Foundation (DFG)GRK1885 Germany
CitationJournal: Nat Commun / Year: 2023
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
DepositionMay 30, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17533.png

Downloads & links

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Map

FileDownload / File: emd_17533.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFAD_ASQ bound blue-light state structure of PdLCry - lowpass filtered to 8 Angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.84 Å		0.86 Å/pix.
x 320 pix.
= 275.84 Å		0.86 Å/pix.
x 320 pix.
= 275.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.3646615 - 1.0691208
Average (Standard dev.)0.00014604008 (±0.019041399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: FAD ASQ bound blue-light state structure of PdLCry - unfiltered map

Fileemd_17533_additional_1.map
AnnotationFAD_ASQ bound blue-light state structure of PdLCry - unfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17533_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17533_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : monomeric PdLCry in the blue-light state

EntireName: monomeric PdLCry in the blue-light state
Components
  • Complex: monomeric PdLCry in the blue-light state
    • Protein or peptide: light receptive cryptochrome

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Supramolecule #1: monomeric PdLCry in the blue-light state

SupramoleculeName: monomeric PdLCry in the blue-light state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Platynereis dumerilii (Dumeril's clam worm)
Molecular weightTheoretical: 65 KDa

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Macromolecule #1: light receptive cryptochrome

MacromoleculeName: light receptive cryptochrome / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Platynereis dumerilii (Dumeril's clam worm)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMBis-tris propane
150.0 mMNaCl
1.0 mMTCEP
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen 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

MicroscopeFEI TITAN KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2 / Details: see material+methods
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen 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

Particle selectionDetails: see supplementary table and materials+methods
Startup modelType of model: OTHER / Details: ab initio (cryoSPARC)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 446759
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8p4x


Chain - Source name: PDB / Chain - Initial model type: experimental model

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