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- EMDB-63034: Cryo-EM structure of human ZAC with A152 mutant in zinc binding state -

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Basic information

Entry
Database: EMDB / ID: EMD-63034
TitleCryo-EM structure of human ZAC with A152 mutant in zinc binding state
Map data
Sample
  • Complex: ZAC in complex with zinc ion
    • Protein or peptide: Ligand-gated cation channel ZACN,Genome polyprotein
  • Ligand: ZINC ION
KeywordsCys-loop receptor / homopentamer / cation channel / zinc-binding state / MEMBRANE PROTEIN
Function / homology
Function and homology information


pH-gated monoatomic ion channel activity / transmembrane transporter complex / response to zinc ion / ligand-gated monoatomic cation channel activity / ligand-gated monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / extracellular ligand-gated monoatomic ion channel activity / bioluminescence / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus ...pH-gated monoatomic ion channel activity / transmembrane transporter complex / response to zinc ion / ligand-gated monoatomic cation channel activity / ligand-gated monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / extracellular ligand-gated monoatomic ion channel activity / bioluminescence / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / generation of precursor metabolites and energy / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / transmembrane signaling receptor activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP 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 / : / Green fluorescent protein, GFP / Picornavirus coat protein / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily ...Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / : / Green fluorescent protein, GFP / Picornavirus coat protein / 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 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Ligand-gated cation channel ZACN
Similarity search - Component
Biological speciesHomo sapiens (human) / Human enterovirus 71
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsQu Q / Zhou Z
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371256 China
National Natural Science Foundation of China (NSFC)32171194 China
National Natural Science Foundation of China (NSFC)32401007 China
CitationJournal: Cell Discov / Year: 2026
Title: Structural basis of human zinc-activated channel (ZAC) signaling and modulation.
Authors: Zixuan Zhou / Yonghui Long / Yulin Chao / Chuanhui Yang / Yi-Quan Tang / Yilai Shu / Hongtao Zhu / Anders A Jensen / Qianhui Qu /
Abstract: Zinc (Zn) plays essential roles in a plethora of physiological processes, including key functions as a neuromodulator. The zinc-activated channel (ZAC) belongs to the Cys-loop receptor (CLR) ...Zinc (Zn) plays essential roles in a plethora of physiological processes, including key functions as a neuromodulator. The zinc-activated channel (ZAC) belongs to the Cys-loop receptor (CLR) superfamily of pentameric ligand-gated ion channels, which also comprises receptors for the important neurotransmitters acetylcholine, serotonin, GABA and glycine. In contrast to these classical CLRs, which have been extensively explored over decades, ZAC remains poorly characterized despite its potential significance in mammals. Here, we present several cryo-EM structures of human ZAC, including the ligand-free resting state, the Zn-bound state, and several antagonist-bound states. In the Zn-bound structure, Zn ions bind to the subunit interfaces of the extracellular domain, corresponding to the canonical agonist-binding sites in the classical CLRs, and are primarily coordinated through cation‒π interactions with two aromatic residues. While the antagonist TTFB inhibits ZAC by insertion between the transmembrane M2 helices of adjacent subunits, d-tubocurarine acts in a dual manner by blocking the channel and interfering with agonist binding. Combined with mutagenesis and electrophysiological analysis, these evaluations highlight the distinctive structural and functional features of this atypical CLR.
History
DepositionJan 7, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63034.png

Downloads & links

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Map

FileDownload / File: emd_63034.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.6944509 - 4.9847016
Average (Standard dev.)-0.00016219301 (±0.15686932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63034_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_63034_half_map_2.map
Projections & Slices
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Sample components

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Entire : ZAC in complex with zinc ion

EntireName: ZAC in complex with zinc ion
Components
  • Complex: ZAC in complex with zinc ion
    • Protein or peptide: Ligand-gated cation channel ZACN,Genome polyprotein
  • Ligand: ZINC ION

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Supramolecule #1: ZAC in complex with zinc ion

SupramoleculeName: ZAC in complex with zinc ion / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ligand-gated cation channel ZACN,Genome polyprotein

MacromoleculeName: Ligand-gated cation channel ZACN,Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Human enterovirus 71
Molecular weightTheoretical: 78.830859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMALWSLLHL TFLGFSITLL LVHGQGFQGT AAIWPSLFNV NLSKKVQESI QIPNNGSAPL LVDVRVFVSN VFNVDILRYT MSSMLLLRL SWLDTRLAWN TSAHPRHAIT LPWESLWTPR LTILEALWVD WRDQSPQARV DQDGHVKLNL ALTTETNCNF E LLHFPRDH ...String:
MMALWSLLHL TFLGFSITLL LVHGQGFQGT AAIWPSLFNV NLSKKVQESI QIPNNGSAPL LVDVRVFVSN VFNVDILRYT MSSMLLLRL SWLDTRLAWN TSAHPRHAIT LPWESLWTPR LTILEALWVD WRDQSPQARV DQDGHVKLNL ALTTETNCNF E LLHFPRDH SNCSLSFYAL SNTAMELEFQ AHVVNEIVSV KREYVVYDLK TQVPPQQLVP CFQVTLRLKN TALKSIIALL VP AEALLLA DVCGGLLPLR AIERIGYKVT LLLSYLVLHS SLVQALPSSS SCNPLLIYYF TILLLLLFLS TIETVLLAGL LAR GNLGAK SGPSPAPRGE QREHGNPGPH PAEEPSRGVK GSQRSWPETA DRIFFLVYVV GVLCTQFVFA GIWMWAACKS DAAP GEAAP HGRRPRLSDL EVLFQGPEFW SHPQFEKGGG SGGGSGGSAW SHPQFEKEFD IDYKDDDDKS RMVSKGEELF TGVVP ILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKFI CTTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYV QER TIFFKDDGNY KTRAEVKFEG DTLVNRIELK GIDFKEDGNI LGHKLEYNYN SHNVYIMADK QKNGIKVNFK IRHNIED GS VQLADHYQQN TPIGDGPVLL PDNHYLSTQS ALSKDPNEKR DHMVLLEFVT AAGITLGMDE LYK

UniProtKB: Ligand-gated cation channel ZACN, Genome polyprotein

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 5 / 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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 260.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 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: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63112
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9leu:
Cryo-EM structure of human ZAC with A152 mutant in zinc binding state

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