{"doi":"10.1101/2020.04.16.045674","title":"Employing NaChBac for cryo-EM analysis of toxin action on voltage-gated Na <sup>+</sup> channels in nanodisc","abstract":"Abstract NaChBac, the first bacterial voltage-gated Na + (Na v ) channel to be characterized, has been the prokaryotic prototype for studying the structure-function relationship of Na v channels. Discovered nearly two decades ago, the structure of NaChBac has not been determined. Here we present the cryo-EM analysis of NaChBac in both detergent micelles and nanodiscs. Under both conditions, the conformation of NaChBac is nearly identical to that of the potentially inactivated Na v Ab. Determining the structure of NaChBac in nanodiscs enabled us to examine gating modifier toxins (GMTs) of Na v channels in lipid bilayers. To study GMTs in mammalian Na v s, we generated a chimera in which the extracellular fragment of the S3 and S4 segments in the second voltage-sensing domain from Na v 1.7 replaces the corresponding sequence in NaChBac. Cryo-EM structures of the nanodisc-embedded chimera alone and in complex with HuwenToxin IV (HWTX-IV) were determined to 3.5 Å and 3.2 Å resolutions, respectively. Compared to the structure of HWTX-IV-bound human Na v 1.7, which was obtained at an overall resolution of 3.2 Å, the local resolution of the toxin has been improved from ~ 6 Å to ~ 4 Å. This resolution enabled visualization of toxin docking. NaChBac can thus serve as a convenient surrogate for structural studies of the interactions between GMTs and Na v channels in a membrane environment.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":121539,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.951,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":561025,"name":"William C. Valinsky","orcid":"0000-0001-7736-9146","position":1,"is_corresponding":false},{"id":561467,"name":"Nguyen Cam On","orcid":null,"position":2,"is_corresponding":false},{"id":561026,"name":"Patrick R. Houlihan","orcid":"0000-0002-2505-2347","position":3,"is_corresponding":false},{"id":561027,"name":"Qian Qu","orcid":"0000-0003-4648-1869","position":4,"is_corresponding":false},{"id":561028,"name":"Lei Liu","orcid":"0000-0001-6290-8602","position":5,"is_corresponding":false},{"id":489829,"name":"Xiaojing Pan","orcid":"0000-0003-1882-5361","position":6,"is_corresponding":false},{"id":561029,"name":"David E. Clapham","orcid":"0000-0002-4459-9428","position":7,"is_corresponding":false},{"id":256562,"name":"Nieng Yan","orcid":"0000-0003-4829-7416","position":8,"is_corresponding":false},{"id":296080,"name":"Shuai Gao","orcid":"0000-0002-8734-2489","position":0,"is_corresponding":true}],"reference_count":61,"raw_metadata":null,"created_at":"2026-07-18T23:14:42.734024Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}