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- EMDB-39648: Structure of a Cys-loop Receptor in Zinc Binding State -

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Basic information

Entry
Database: EMDB / ID: EMD-39648
TitleStructure of a Cys-loop Receptor in Zinc Binding State
Map dataEM_map
Sample
  • Complex: Cys-loop Receptor in Zinc Binding State
    • Protein or peptide: Ligand-gated cation channel ZACN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsCys-loop Receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


pH-gated monoatomic ion channel activity / transmembrane transporter complex / response to zinc ion / ligand-gated monoatomic ion channel activity / 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: 2.9 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 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39648.png

Downloads & links

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Map

FileDownload / File: emd_39648.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM_map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 260.4 Å		0.93 Å/pix.
x 280 pix.
= 260.4 Å		0.93 Å/pix.
x 280 pix.
= 260.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.38108474 - 0.72546595
Average (Standard dev.)0.0012605902 (±0.023961361)
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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Half map: Half map B

Fileemd_39648_half_map_1.map
AnnotationHalf_map_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_39648_half_map_2.map
AnnotationHalf_map_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cys-loop Receptor in Zinc Binding State

EntireName: Cys-loop Receptor in Zinc Binding State
Components
  • Complex: Cys-loop Receptor in Zinc Binding State
    • Protein or peptide: Ligand-gated cation channel ZACN
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Cys-loop Receptor in Zinc Binding State

SupramoleculeName: Cys-loop Receptor in Zinc Binding State / 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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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41800
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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