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- EMDB-17429: FAD_ox bound dark state structure of PdLCry -

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Basic information

Entry
Database: EMDB / ID: EMD-17429
TitleFAD_ox bound dark state structure of PdLCry
Map datastructure of FAD_ox bound dark state PdLCry
Sample
  • Complex: dimeric complex of PdLCry in the dark state
    • Protein or peptide: Putative light-receptive cryptochrome (Fragment)
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordslight-sensitive / circalunar clock / FLAVOPROTEIN
Function / homology
Function and homology information


Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Putative light-receptive cryptochrome
Similarity search - Component
Biological speciesPlatynereis dumerilii (Dumeril's clam worm)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 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 23, 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_17429.png

Downloads & links

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Map

FileDownload / File: emd_17429.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of FAD_ox bound dark state PdLCry
Voxel sizeX=Y=Z: 0.862 Å
Density
Contour LevelBy AUTHOR: 1.75
Minimum - Maximum-6.2337594 - 10.444278000000001
Average (Standard dev.)-0.0008216328 (±0.18919145)
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: structure of FAD ox bound dark state PdLCry with...

Fileemd_17429_additional_1.map
Annotationstructure of FAD_ox bound dark state PdLCry with local resolution filter applied
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: structure of FAD ox bound dark state PdLCry - odd particles

Fileemd_17429_half_map_1.map
Annotationstructure of FAD_ox bound dark state PdLCry - odd particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: structure of FAD ox bound dark state PdLCry - even particles

Fileemd_17429_half_map_2.map
Annotationstructure of FAD_ox bound dark state PdLCry - even particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dimeric complex of PdLCry in the dark state

EntireName: dimeric complex of PdLCry in the dark state
Components
  • Complex: dimeric complex of PdLCry in the dark state
    • Protein or peptide: Putative light-receptive cryptochrome (Fragment)
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: dimeric complex of PdLCry in the dark state

SupramoleculeName: dimeric complex of PdLCry in the dark state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Platynereis dumerilii (Dumeril's clam worm)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Putative light-receptive cryptochrome (Fragment)

MacromoleculeName: Putative light-receptive cryptochrome (Fragment) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Platynereis dumerilii (Dumeril's clam worm)
Molecular weightTheoretical: 65.482855 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKEKMSAWEV GNGIMEEKTD DWDNKEDNGK EHVSLHWFRH GLRLHDNPAL LKSLEGAKEF YALFIWDGEV AGTKLVSYPR MKFLLECLK DLDDSLKKHG GRLYVVKGPS DVVIKQLIEE WGVTRVTCEI DPEPIWQPRD KAVKDLCATK GVKWFDYNSH L LWDPKAVC ...String:
MKEKMSAWEV GNGIMEEKTD DWDNKEDNGK EHVSLHWFRH GLRLHDNPAL LKSLEGAKEF YALFIWDGEV AGTKLVSYPR MKFLLECLK DLDDSLKKHG GRLYVVKGPS DVVIKQLIEE WGVTRVTCEI DPEPIWQPRD KAVKDLCATK GVKWFDYNSH L LWDPKAVC DANGGRPPHT YKLFCQVTDL LGKPETPHPD PDFSHVQMPV SDDFDDKFGL PTLKELGCEP ECEEQEKPFN KW QGGETGA LELLETRLMI ERTAYKAGYI MPNQYIPDLV GPPRSMSPHL RFGALSIRKF YWDLHNNYAE VCGGEWLGAL TAQ LVWREY FYCMSYGNPS FDKMEGNPIC LQIPWYKDEE ALEKWKQGQT GFPWIDACMR QLRYEGWMHH VGRHAVACFL TRGD LWISW VDGLEAFYKY MLDGDWSVCA GNWMWVSSSA FENCLQCPQC FSPVLYGMRM DPTGEFTRRY VPQLKNMPLK YLFQP WKAP KEVQEKAGCV IGEDYPSPMV DHKEASSKCR RMMEDVKSII KDPEVWHCTP SDTNEVRKFC WLPEHMTADQ PCLGDL PCI KY

UniProtKB: Putative light-receptive cryptochrome

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 84 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
0.01 %fOM
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 prepared under far-red light illumination.
Detailsgrids were prepared under far-red light illumination (Osram OSLON SSL 120, GF CSSPM1.24)

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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 opticsIllumination 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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 424744
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 modelChain - Source name: Other / Chain - Initial model type: integrative model / Details: starting model was based on 4jzy
SoftwareName: Coot
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8p4x:
FAD_ox bound dark state structure of PdLCry

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