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- PDB-8yq5: Cryo-EM structure of a de novo designed transmembrane protein tmZ... -

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Entry
Database: PDB / ID: 8yq5
TitleCryo-EM structure of a de novo designed transmembrane protein tmZC8-BTB
Componentsde novo designed ion channel
KeywordsDE NOVO PROTEIN / De novo design / Ion channels
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLu, P.L. / Zhou, C.
Funding support China, 1items
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
DepositionMar 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
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Revision 1.1Oct 29, 2025Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: de novo designed ion channel
D: de novo designed ion channel
C: de novo designed ion channel
B: de novo designed ion channel
A: de novo designed ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,03411
Polymers130,9705
Non-polymers3,0646
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
de novo designed ion channel


Mass: 26194.074 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: De novo design of Ion channels / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.1_4122: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 523672 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038412
ELECTRON MICROSCOPYf_angle_d0.5911350
ELECTRON MICROSCOPYf_dihedral_angle_d12.9123084
ELECTRON MICROSCOPYf_chiral_restr0.0381374
ELECTRON MICROSCOPYf_plane_restr0.0031345

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