AlphaFold Predictions, Integrative Structural Model, Native Mass Spectrometry and Mass Photometry Data for the Human Norovirus GI NS3 Complex

Abstract

This dataset contains the AlphaFold2, AlphaFold3 and integrative structural models, together with native mass spectrometry and mass photometry data, underlying Haas et al., “Integrative structure of norovirus NS3 suggests a role in RNA transport”. Norovirus NS3 is a membrane-bound AAA+ ATPase of superfamily 3 (SF3). The associated study reports the cryo-EM structure of a soluble, hexameric, catalytically active NS3 construct and combines it with structure prediction to build a full-length, membrane-associated model in which NS3 forms a continuous conduit across the membrane. Native mass spectrometry and mass photometry were used to characterise the oligomeric state of the recombinant NS3 constructs. The dataset is organised into nine groups of files, together with a README file: 01 – AlphaFold2 MultimerAlphaFold2-Multimer prediction of the full-length human norovirus GI NS3 hexamer, used for construct design and selection of the ΔN61 truncation site. 02 – AlphaFold3 nucleic-acid predictionsAlphaFold3 predictions of the ΔN61 NS3 hexamer bound to nucleic acid, ATP and Mg²⁺, comparing a 50-nt poly(A) ssRNA substrate with the equivalent 50-nt poly(dA) ssDNA substrate. 03 – AlphaFold3 full-length GI and GV predictionsAlphaFold3 predictions of full-length GI and GV NS3 hexamers, with and without 50 oleic acid molecules to mimic a membrane-like environment. 04 – AlphaFold3 oligomeric-state scansAlphaFold3 subunit-number scans across norovirus genogroups I to V, containing predictions with 1–10 NS3 copies and used to compare interface predicted template modelling (iPTM) scores as a function of oligomeric state. 05 – AlphaFold3 N-terminal fragment predictionsAlphaFold3 predictions of monomeric NS3 N-terminal fragments across norovirus genogroups I to V, corresponding to truncation-based comparisons with the previously proposed MLKL-like fold. 06 – AlphaFold3 NS3 and enterovirus 2C comparisonAlphaFold3 predictions of the full-length human norovirus GI NS3 hexamer and the full-length Coxsackievirus B3 2C hexamer in a membrane-mimicking environment with poly(A) RNA, ATP and Mg²⁺. 07 – Integrative structural modelThe final full-length human norovirus GI NS3 integrative model, combining the experimentally determined cryo-EM structure of the AAA+ and helical bundle regions with the AlphaFold3-derived N-terminal membrane-associated region. 08 – Native mass spectrometryNative mass spectrometry data used to characterise the oligomeric state of recombinant human norovirus GI NS3 constructs. The archive contains the available experimental and processed data associated with the native mass spectrometry analysis, together with supporting information describing the relationship between deposited files and the corresponding manuscript data. 09 – Mass photometryMass photometry data used to characterise the oligomeric state of recombinant human norovirus GI NS3 constructs. The archive contains the available experimental and processed data, including data supporting the mass distributions reported in the manuscript, together with supporting information describing the deposited files. A README provides an overview of the complete Zenodo deposition, describes the organisation of the individual archives and maps the deposited datasets to the corresponding experiments and manuscript figures. The structural modelling archives are organised by modelling experiment and, where applicable, by manuscript figure. Deposited modelling files include coordinate files, prediction input or job-definition files, ranked AlphaFold model outputs, summary confidence files, full confidence data containing pLDDT and predicted aligned error information, and README files describing the contents of individual archives. Multiple sequence alignments and structural templates are included where retained from the original prediction run. The file Haas_et_al_NS3_models_Supplementary_Data_07_HuNoV_GI_NS3_full_length_integrative_model.pdb represents the final membrane-associated integrative model shown in the manuscript. In this model, the predicted N-terminal transmembrane region aligns with the helical bundle and AAA+ ATPase domains to form a continuous central channel. The model was used to visualise the proposed RNA translocation pathway across replication organelle membranes and supports the structural interpretation presented in the associated manuscript. Related depositions from the same study include Protein Data Bank entry 9R34, Electron Microscopy Data Bank entry EMD-53547, and Electron Microscopy Public Image Archive entry EMPIAR-12758.