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- EMDB-39649: Structure of a Cys-loop Receptor under Acidic Condition -

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Basic information

Entry
Database: EMDB / ID: EMD-39649
TitleStructure of a Cys-loop Receptor under Acidic Condition
Map dataEM_map
Sample
  • Complex: Cys-loop Receptor under Acidic Condition
    • Protein or peptide: Ligand-gated cation channel ZACN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCys-loop Receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


pH-gated monoatomic ion channel activity / transmembrane transporter complex / ligand-gated monoatomic ion channel activity / response to zinc ion / ligand-gated monoatomic cation channel activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / monoatomic ion transmembrane transport / zinc ion binding / plasma membrane
Similarity search - Function
Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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
Ligand-gated cation channel ZACN
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLu XH / Yang X / Shen YQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the activation mechanism of the human zinc-activated channel.
Authors: Xuhang Lu / Dongmei Li / Yaojie Wang / Gaohua Zhang / Tianlei Wen / Yue Lu / Nan Jia / Xuedi Wang / Shenghai Chang / Xing Zhang / Jianping Lin / Yu-Hang Chen / Xue Yang / Yuequan Shen /
Abstract: The zinc-activated channel (ZAC) is an atypical mammalian cys-loop receptor (CLR) that is activated by zinc ions and protons, allowing cations to pass through. The molecular mechanism that ligands ...The zinc-activated channel (ZAC) is an atypical mammalian cys-loop receptor (CLR) that is activated by zinc ions and protons, allowing cations to pass through. The molecular mechanism that ligands use to activate ZAC remains elusive. Here, we present three cryo-electron microscopy reconstructions of human ZAC (hZAC) under different conditions. These three hZAC structures display highly similar conformations to one another, forming symmetrical homo-pentamers with a central ion-conduction pore. The hZAC protomer comprises an extracellular domain (ECD) and a transmembrane domain (TMD), sharing more structural similarity with anion-permeable CLRs, such as glycine receptors and type A γ-aminobutyric acid receptors. Notably, hZAC possesses a distinctive C-tail that establishes a disulfide bond with the loop M2-M3 in the TMD and occupies what is typically the canonical neurotransmitter orthosteric site in other mammalian CLRs. Moreover, the tip of the cys-loop creates an unprecedented orthosteric site in hZAC. The binding of Zn triggers a conformational shift in the cys-loop, which presumably prompts the loop M2-M3 to move and open the channel gate. This study sheds light on the assembly of the channel, its structural features, and the process of signal transduction in hZAC.
History
DepositionApr 2, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_39649.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM_map
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.37260404 - 0.8001657
Average (Standard dev.)0.0013945448 (±0.024476964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cys-loop Receptor under Acidic Condition

EntireName: Cys-loop Receptor under Acidic Condition
Components
  • Complex: Cys-loop Receptor under Acidic Condition
    • Protein or peptide: Ligand-gated cation channel ZACN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cys-loop Receptor under Acidic Condition

SupramoleculeName: Cys-loop Receptor under Acidic Condition / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230 KDa

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Macromolecule #1: Ligand-gated cation channel ZACN

MacromoleculeName: Ligand-gated cation channel ZACN / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.858117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMALWSLLHL TFLGFSITLL LVHGQGFQGT AAIWPSDYKD DDDKLFNVNL SKKVQESIQI PNNGSAPLLV DVRVFVSNVF NVDILRYTM SSMLLLRLSW LDTRLAWNTS AHPRHAITLP WESLWTPRLT ILEALWVDWR DQSPQARVDQ DGHVKLNLAL A TETNCNFE ...String:
MMALWSLLHL TFLGFSITLL LVHGQGFQGT AAIWPSDYKD DDDKLFNVNL SKKVQESIQI PNNGSAPLLV DVRVFVSNVF NVDILRYTM SSMLLLRLSW LDTRLAWNTS AHPRHAITLP WESLWTPRLT ILEALWVDWR DQSPQARVDQ DGHVKLNLAL A TETNCNFE LLHFPRDHSN CSLSFYALSN TAMELEFQAH VVNEIVSVKR EYVVYDLKTQ VPPQQLVPCF QVTLRLKNTA LK SIIALLV PAEALLLADV CGGLLPLRAI ERIGYKVTLL LSYLVLHSSL VQALPSSSSC NPLLIYYFTI LLLLLFLSTI ETV LLAGLL ARGNLGAKSG PSPAPRGEQR EHGNPGPHPA EEPSRGVKGS QRSWPETADR IFFLVYVVGV LCTQFVFAGI WMWA ACKSD AAPGEAAPHG RRPRL

UniProtKB: Ligand-gated cation channel ZACN

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
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: 1.3 µm
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

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39879
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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