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- EMDB-68608: Cryo-EM structure of the Deg-3/Des-2 betaine-bound intermediate state -

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Basic information

Entry
Database: EMDB / ID: EMD-68608
TitleCryo-EM structure of the Deg-3/Des-2 betaine-bound intermediate state
Map data
Sample
  • Complex: Deg-3/Des-2 complex with betaine
    • Protein or peptide: Acetylcholine receptor subunit alpha-type des-2
    • Protein or peptide: Acetylcholine receptor subunit alpha-type deg-3
  • Ligand: TRIMETHYL GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsnAChR / Betaine / MEMBRANE PROTEIN
Function / homology
Function and homology information


Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Neurotransmitter receptors and postsynaptic signal transmission / regulation of programmed cell death / positive regulation of locomotion involved in locomotory behavior / excitatory extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / transmembrane signaling receptor activity / chemical synaptic transmission ...Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Neurotransmitter receptors and postsynaptic signal transmission / regulation of programmed cell death / positive regulation of locomotion involved in locomotory behavior / excitatory extracellular ligand-gated monoatomic ion channel activity / transmembrane transporter complex / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / transmembrane signaling receptor activity / chemical synaptic transmission / monoatomic ion transmembrane transport / neuron projection / postsynapse / postsynaptic membrane / synapse / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha-type des-2 / Acetylcholine receptor subunit alpha-type deg-3
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsNing Y / Ge J / Yu J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis of ligand recognition and gating in a heteromeric Deg-3/Des-2 nicotinic acetylcholine receptor.
Authors: Yingjie Ning / Qiqi Jiang / Zizhuo Lu / Jie Yu / Jingpeng Ge /
Abstract: During evolution, nicotinic acetylcholine receptors (nAChRs) have diversified in subunit composition and ligand selectivity, enabling a conserved ion channel scaffold to support a broad range of ...During evolution, nicotinic acetylcholine receptors (nAChRs) have diversified in subunit composition and ligand selectivity, enabling a conserved ion channel scaffold to support a broad range of signaling functions beyond classical synaptic transmission. Deg-3/Des-2 is a nematode-specific, calcium-permeable heteromeric α-type nicotinic receptor in sensory neurons to mediate chemosensation, nociception, and mechanotransduction, and represents a promising anthelmintic target. Here, we report cryo-electron microscopy structures of Deg-3/Des-2 in its apo, agonist-bound intermediate and agonist-bound open states. Deg-3/Des-2 adopts a 2Deg-3:3Des-2 stoichiometry. Five agonist molecules occupy intersubunit orthosteric sites, driving channel opening primarily through rotational rearrangements of the upper M2 helices that relieve a conserved hydrophobic gate and enable calcium permeation. We further identify a Deg-3-specific N-terminal helix that regulates desensitization and a negatively charged extracellular vestibular helix that governs calcium permeability. Together, these structures reveal how evolutionary tuning of ligand recognition, ion selectivity, and gating within a conserved nicotinic receptor framework.
History
DepositionJan 21, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68608.png

Downloads & links

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Map

FileDownload / File: emd_68608.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å		1.06 Å/pix.
x 300 pix.
= 316.5 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.29
Minimum - Maximum-2.2949772 - 2.935539
Average (Standard dev.)-0.00052488624 (±0.08685682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.49997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68608_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68608_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Deg-3/Des-2 complex with betaine

EntireName: Deg-3/Des-2 complex with betaine
Components
  • Complex: Deg-3/Des-2 complex with betaine
    • Protein or peptide: Acetylcholine receptor subunit alpha-type des-2
    • Protein or peptide: Acetylcholine receptor subunit alpha-type deg-3
  • Ligand: TRIMETHYL GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Deg-3/Des-2 complex with betaine

SupramoleculeName: Deg-3/Des-2 complex with betaine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Acetylcholine receptor subunit alpha-type des-2

MacromoleculeName: Acetylcholine receptor subunit alpha-type des-2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 62.153859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLIIIQSLLL ATTASLCIAD TPVPTQIRLV HDLLDNYDKK AKPMWDNSKP INVSFSMDLY QILELNEPQQ YILLNAWIIE RWFDEFLYW NPDDYENITE LRLPYDSIWL PDTTLYNSLV MKDDDTRRLL NSKLTTDTHR RAALIELLYP TIYKFSCLLD L RFFPFDVQ ...String:
MLIIIQSLLL ATTASLCIAD TPVPTQIRLV HDLLDNYDKK AKPMWDNSKP INVSFSMDLY QILELNEPQQ YILLNAWIIE RWFDEFLYW NPDDYENITE LRLPYDSIWL PDTTLYNSLV MKDDDTRRLL NSKLTTDTHR RAALIELLYP TIYKFSCLLD L RFFPFDVQ VCTMTFSSWT YDQKGIDYFP YSDKIGTSNY LENEGWYILQ TKIKRQEVKY ACCPNNYTLL QLTLYLRRKP LF YLVNLII PTSIITLIAI VGFFTTSSAS GMREEKVSLG ITTLLSMSIL MLMVSDQMPT TSTFIPLIGW FILAMIIVIS LGT VVSSVI IAIQKRGSLG ERMSKRALKF AKVLAWFTCT SLPPHVEKEH MMEAFDAPTP LVEVRPLQLA SVKESVRNKW VSGA RRATQ RGNSGLALIS DKSTDPLIHL SPTAHQPDES ISPSAPPVPS SSPLPPPLTP GPADDVVSVA SELSSKFLTS RMRPK SQKD NTFAAMQSSI KANRQLAVAE FEWFATVVER TCFVIFVVAF LIITFGINFI GFIHWHQAGV EYGG

UniProtKB: Acetylcholine receptor subunit alpha-type des-2

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Macromolecule #2: Acetylcholine receptor subunit alpha-type deg-3

MacromoleculeName: Acetylcholine receptor subunit alpha-type deg-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 64.99698 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTLKIRTIII LFCVISVTTT SQSLNATLKT FDPRLLNSTA DRDIAMKNVP LVRLTRHLLS PERYDVRVRP ILDHKKSLKV HISISLYQI IEVDEPSQNI KLNVWMIQKW RDEYLDWNPN EYGMINSTII PFHHLWIPDT YLYNSVKMSR DETERYMNIQ A TSNYWKGE ...String:
MTLKIRTIII LFCVISVTTT SQSLNATLKT FDPRLLNSTA DRDIAMKNVP LVRLTRHLLS PERYDVRVRP ILDHKKSLKV HISISLYQI IEVDEPSQNI KLNVWMIQKW RDEYLDWNPN EYGMINSTII PFHHLWIPDT YLYNSVKMSR DETERYMNIQ A TSNYWKGE KGAELSFLYP AIYTITCRLN IRFFPYDRQN CTLTISSWTN SKSALDYYAD TEVSMQSFIP NEEWQVKSFK IH RHEYKYA CCAEPWVILQ ASLVIQRKPL YYLVNLIIPT SIITLVAITG FFTPASTDDD RTEKINLGIT TLLAMSILML MVS DQMPTT SEFVPLIAWF YLSIIIIISI GTFLTSVVLS VQGRRQYGRN PPQFIRYIFF VLLPQVLLLN VPPPLQTLWG ELDD DPLNV RRRKKSHYLS RNVNNGSTKM ASPMSTLRVP QSAGSVSEKR QSFQMIDVTS PNSPNTARSR APSLAPSTAK ATMWE GTMS ALAGTNTQLR RTSNVFNKEV DEMRRKRQCS LEWEFLATVL DRFLLIVFVG AVVIVTAGLI LVGRMAQYSY DHPDDR FFN V

UniProtKB: Acetylcholine receptor subunit alpha-type deg-3

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Macromolecule #5: TRIMETHYL GLYCINE

MacromoleculeName: TRIMETHYL GLYCINE / type: ligand / ID: 5 / Number of copies: 5 / Formula: BET
Molecular weightTheoretical: 118.154 Da
Chemical component information

ChemComp-BET:
TRIMETHYL GLYCINE

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 5 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 174261
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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