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- EMDB-60471: Cryo-EM structure of the ZAC zinc-activated channel in amphipol -

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Basic information

Entry
Database: EMDB / ID: EMD-60471
TitleCryo-EM structure of the ZAC zinc-activated channel in amphipol
Map data
Sample
  • Complex: ZAC pentamer
    • Protein or peptide: ZAC
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsTRANSPORT PROTEIN
Biological speciesOryzias latipes (Japanese medaka)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsJin F / Hattori M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Cryo-EM structure of the zinc-activated channel (ZAC) in the Cys-loop receptor superfamily.
Authors: Fei Jin / Yi-Yu Lin / Ru-Chun Wang / Tang-Xuan Xie / Yimeng Zhao / Cheng Shen / Danqi Sheng / Muneyoshi Ichikawa / Ye Yu / Jin Wang / Motoyuki Hattori /
Abstract: Cys-loop receptors are a large superfamily of pentameric ligand-gated ion channels with various physiological roles, especially in neurotransmission in the central nervous system. Among them, zinc- ...Cys-loop receptors are a large superfamily of pentameric ligand-gated ion channels with various physiological roles, especially in neurotransmission in the central nervous system. Among them, zinc-activated channel (ZAC) is a Zn-activated ion channel that is widely expressed in the human body and is conserved among eukaryotes. Due to its gating by extracellular Zn, ZAC has been considered a Zn sensor, but it has undergone minimal structural and functional characterization since its molecular cloning. Among the families in the Cys-loop receptor superfamily, only the structure of ZAC has yet to be determined. Here, we determined the cryo-EM structure of ZAC in the apo state and performed structure-based mutation analyses. We identified a few residues in the extracellular domain whose mutations had a mild impact on Zn sensitivity. The constriction site in the ion-conducting pore differs from the one in other Cys-loop receptor structures, and further mutational analysis identified a key residue that is important for ion selectivity. In summary, our work provides a structural framework for understanding the ion-conducting mechanism of ZAC.
History
DepositionJun 7, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60471.png

Downloads & links

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Map

FileDownload / File: emd_60471.map.gz / Format: CCP4 / Size: 64 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.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.039936397 - 0.075820744
Average (Standard dev.)0.00027501318 (±0.003182538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60471_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_60471_half_map_2.map
Projections & Slices
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Sample components

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Entire : ZAC pentamer

EntireName: ZAC pentamer
Components
  • Complex: ZAC pentamer
    • Protein or peptide: ZAC
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: ZAC pentamer

SupramoleculeName: ZAC pentamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryzias latipes (Japanese medaka)

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Macromolecule #1: ZAC

MacromoleculeName: ZAC / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Oryzias latipes (Japanese medaka)
Molecular weightTheoretical: 47.255855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKRTPLLVAF LILVLGSGTV DSTCTTRRCL AQMLIDMEML SMPQDENCTL PIYVPFIEYQ TLSVNTKSLR LNSRLRAIVK WTDPQLAWD TSVYPYDAVM LPVDKIWTPV LQVKNGISTN MKHDANDLLV YSNGTVNHEV QINAEINCEV NLFNYPFAGD E CPVAIETF ...String:
MKRTPLLVAF LILVLGSGTV DSTCTTRRCL AQMLIDMEML SMPQDENCTL PIYVPFIEYQ TLSVNTKSLR LNSRLRAIVK WTDPQLAWD TSVYPYDAVM LPVDKIWTPV LQVKNGISTN MKHDANDLLV YSNGTVNHEV QINAEINCEV NLFNYPFAGD E CPVAIETF SSGECVTTLI LDQVRSLDGS TGDWQTTYAR LKKQREDRNF IAVGLKINYS SPLMTLLLPT VLIVLADFVS FA LPLHGGG RNGFKVTLVL SFVMFLNLLN SQLPGNGDCS PIIRIHFCIC LVLLVLSMLV SMVLTRLAHD GSLAFFSPSK RQA PQNTKD NEKKDEEELK ADIHVVLPDG PEDVQMLRKV VTFLQRLDDQ KNQNERKHAF ADKLDKIFFL FYVILGLIYM CVML GIMVA YKCEIDHFNF WY

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

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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 2.3000000000000003 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: OTHER / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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