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- EMDB-63538: Cryo-EM structure of dVGAC complexed with iodide -

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Basic information

Entry
Database: EMDB / ID: EMD-63538
TitleCryo-EM structure of dVGAC complexed with iodide
Map data
Sample
  • Complex: De novo design of Ion channels
    • Protein or peptide: de novo designed ion channel
  • Ligand: IODIDE ION
KeywordsDe novo design / Ion channels / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsLu PL / Zhou C
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0909200 China
CitationJournal: Cell / Year: 2025
Title: De novo designed voltage-gated anion channels suppress neuron firing.
Authors: Chen Zhou / Huican Li / Jiaxing Wang / Cheng Qian / Hui Xiong / Zhilin Chu / Qiming Shao / Xuan Li / Shijin Sun / Ke Sun / Aiqin Zhu / Jiawei Wang / Xueqin Jin / Fan Yang / Tamer M Gamal El- ...Authors: Chen Zhou / Huican Li / Jiaxing Wang / Cheng Qian / Hui Xiong / Zhilin Chu / Qiming Shao / Xuan Li / Shijin Sun / Ke Sun / Aiqin Zhu / Jiawei Wang / Xueqin Jin / Fan Yang / Tamer M Gamal El-Din / Bo Li / Jing Huang / Kun Wu / Peilong Lu /
Abstract: Design of ion channels responsive to environmental cues has significant implications in modulating cellular activities and sensor development, but it remains a significant challenge due to the ...Design of ion channels responsive to environmental cues has significant implications in modulating cellular activities and sensor development, but it remains a significant challenge due to the complexities involved in designing stimuli-induced conformational changes in proteins. Here, we report the accurate de novo design of voltage-gated anion channels, namely dVGACs. dVGACs adopt a 15-helix pentameric architecture featuring arginine constrictions within the transmembrane span and show voltage-dependent anions currents in patch-clamp experiments. Cryo-electron microscopy (cryo-EM) structures of dVGACs closely align with the design models. Cryo-EM structures and molecular dynamics simulations suggest that the arginine constrictions undergo voltage-induced conformational changes, serving as both a voltage sensor and a selectivity filter as designed. Notably, the anion selectivity and voltage sensitivity of dVGACs can be tuned through targeted mutations for suppressing neuronal firing in situ. The ability to create ion channels with custom-designed conformational changes refreshes our insights into membrane biophysics and unveils diverse potential applications.
History
DepositionFeb 23, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63538.png

Downloads & links

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Map

FileDownload / File: emd_63538.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å		1.09 Å/pix.
x 192 pix.
= 208.704 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.493
Minimum - Maximum-2.9216764 - 4.2399635
Average (Standard dev.)0.00936504 (±0.12791806)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 208.70401 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63538_msk_1.map
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Half map: #2

Fileemd_63538_half_map_1.map
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Half map: #1

Fileemd_63538_half_map_2.map
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Sample components

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Entire : De novo design of Ion channels

EntireName: De novo design of Ion channels
Components
  • Complex: De novo design of Ion channels
    • Protein or peptide: de novo designed ion channel
  • Ligand: IODIDE ION

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Supramolecule #1: De novo design of Ion channels

SupramoleculeName: De novo design of Ion channels / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: de novo designed ion channel

MacromoleculeName: de novo designed ion channel / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 26.424367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHHHHHHSS GENLYFQGSS NANAPVHIDV GGHMYTSSLA TLTKYPESRI GRLFDGTEPI VLDSLKQHYF IDRDGQMFRY ILNFLRTSK LLIPDDFKDY TLLYEEAKYF QLQPMLLEME RWKQDEERGK GAGVEILLKI IILIIFAVIV AAAAILWALK A KALTVVTM ...String:
MSHHHHHHSS GENLYFQGSS NANAPVHIDV GGHMYTSSLA TLTKYPESRI GRLFDGTEPI VLDSLKQHYF IDRDGQMFRY ILNFLRTSK LLIPDDFKDY TLLYEEAKYF QLQPMLLEME RWKQDEERGK GAGVEILLKI IILIIFAVIV AAAAILWALK A KALTVVTM LLGVLLFLVR LAIRFFIRVI ERLLKEGKEE EAEKLAKKLV LFIALFVLFI IMVVWALMKL L

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Macromolecule #2: IODIDE ION

MacromoleculeName: IODIDE ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: IOD
Molecular weightTheoretical: 126.904 Da
Chemical component information

ChemComp-IOD:
IODIDE ION

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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: 1.4000000000000001 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: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 441996
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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