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Open data
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Basic information
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Title | FMRFa-bound Malacoceros FaNaC1 in lipid nanodiscs | ||||||||||||
![]() | deepEMhancer postprocessed FMRFa-bound FaNaC1 map, used in model building and figure preparation | ||||||||||||
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![]() | Neuropeptide / ion channel / DEG/ENaC / MEMBRANE PROTEIN | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||
![]() | Kalienkova V / Dandamudi M / Paulino C / Lynagh T | ||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Structural basis for excitatory neuropeptide signaling. Authors: Valeria Kalienkova / Mowgli Dandamudi / Cristina Paulino / Timothy Lynagh / ![]() ![]() ![]() Abstract: Rapid signaling between neurons is mediated by ligand-gated ion channels, cell-surface proteins with an extracellular ligand-binding domain and a membrane-spanning ion channel domain. The ...Rapid signaling between neurons is mediated by ligand-gated ion channels, cell-surface proteins with an extracellular ligand-binding domain and a membrane-spanning ion channel domain. The degenerin/epithelial sodium channel (DEG/ENaC) superfamily is diverse in terms of its gating stimuli, with some DEG/ENaCs gated by neuropeptides, and others gated by pH, mechanical force or enzymatic activity. The mechanism by which ligands bind to and activate DEG/ENaCs is poorly understood. Here we dissected the structural basis for neuropeptide-gated activity of a neuropeptide-gated DEG/ENaC, FMRFamide-gated sodium channel 1 (FaNaC1) from the annelid worm Malacoceros fuliginosus, using cryo-electron microscopy. Structures of FaNaC1 in the ligand-free resting state and in several ligand-bound states reveal the ligand-binding site and capture the ligand-induced conformational changes of channel gating, which we verified with complementary mutagenesis experiments. Our results illuminate channel gating in DEG/ENaCs and offer a structural template for experimental dissection of channel pharmacology and ion conduction. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.1 KB 23.1 KB | Display Display | ![]() |
Images | ![]() | 99 KB | ||
Masks | ![]() | 40.6 MB | ![]() | |
Filedesc metadata | ![]() | 7.2 KB | ||
Others | ![]() ![]() ![]() | 30.9 MB 31.1 MB 31.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8on7MC ![]() 8on8C ![]() 8on9C ![]() 8onaC 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 | deepEMhancer postprocessed FMRFa-bound FaNaC1 map, used in model building and figure preparation | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.022 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: refined FMRFa-bound FaNaC1 map, used in model refinement
File | emd_16981_additional_1.map | ||||||||||||
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Annotation | refined FMRFa-bound FaNaC1 map, used in model refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: FMRFa-bound FaNaC1 refined halfmap1
File | emd_16981_half_map_1.map | ||||||||||||
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Annotation | FMRFa-bound FaNaC1 refined halfmap1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: FMRFa-bound FaNaC1 refined halfmap2
File | emd_16981_half_map_2.map | ||||||||||||
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Annotation | FMRFa-bound FaNaC1 refined halfmap2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : FMRFamide-gated sodium channel 1 (FaNaC1)
Entire | Name: FMRFamide-gated sodium channel 1 (FaNaC1) |
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Components |
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-Supramolecule #1: FMRFamide-gated sodium channel 1 (FaNaC1)
Supramolecule | Name: FMRFamide-gated sodium channel 1 (FaNaC1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 205 KDa |
-Macromolecule #1: FMRFamide-gated sodium channel 1 (FaNaC1)
Macromolecule | Name: FMRFamide-gated sodium channel 1 (FaNaC1) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 68.605836 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSAIRDVMTK FAEQTTMHGV PKVINAKSSM GRLFWSLVCL AAGAMFCLQM SEVLQRYFSY PKKVTVEVVP TPVPFPSISI CNMRNLDVH ILNTLNRMFI EDDRPFSNIN KSEHEFIRAY MKKVAKYAPL FWNYQDEYPE VFQEIFSRTT FSANIDPEVI A LAAVQLEG ...String: MSAIRDVMTK FAEQTTMHGV PKVINAKSSM GRLFWSLVCL AAGAMFCLQM SEVLQRYFSY PKKVTVEVVP TPVPFPSISI CNMRNLDVH ILNTLNRMFI EDDRPFSNIN KSEHEFIRAY MKKVAKYAPL FWNYQDEYPE VFQEIFSRTT FSANIDPEVI A LAAVQLEG FVVNCHYAGH RCNKTRDFYR FFDPYYFNCF TYKAHEPTDI EDNLSEGIEN GWSSILLSGS GMLDKNDEIR ML PGLHEWR SAVSASEGVR VVIHPPSTTP YPFTEGYDVP PGFSASFGIH PRRNIRIGPP HGNCSDKNPF GDGTERYRLM ACQ KMCMQH YIVETCGCAD VGLPKLPLQA NISWCRDDDN FPDECMFTAS EECLQLLMQL HNRIKCARSI KSKITKNTTA MEAC NCFPP CDEVSYDVSY SLSKWPSAGY EGDAAYFDVF GIEKFNERFN KTGTQGKYEL FTKYFNVSNR EESMKDFARL NVYIA DSNV VKTQESEDYT RNQLVSDIGG QLGLWVGISL ITLAEVLELI IDLFRLFSKH TYRSVPVIRQ SIKYKDKRNG AEMNYD TRY SQSNGGPHAR YLHHGHSIPK HPPELPDTSL ALEVLFQ |
-Macromolecule #2: FMRFamide, neuropeptide
Macromolecule | Name: FMRFamide, neuropeptide / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 598.76 Da |
Sequence | String: FMRF(NH2) |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.44 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: at 5 mA | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | nanodisc-reconstituted Malacoceros FaNaC1 bound to the full agonist (FMRFamide) |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 90.0 K / Max: 105.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 2 / Number real images: 4479 / Average exposure time: 9.0 sec. / Average electron dose: 50.11 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 49407 / 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: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL |
Output model | ![]() PDB-8on7: |