DOI: 10.5061/dryad.0mv6t
title: Data from: Characterization of C-ring component assembly in flagellar motors from amino acid coevolution

description: Bacterial flagellar motility, an important virulence factor, is energized
 by a rotary motor localized within the flagellar basal body. The rotor
 module consists of a large framework (C-ring), composed of the FliG, FliM
 and FliN proteins. FliN and FliM contacts the FliG torque ring to control
 the direction of flagellar rotation. We report that structure-based models
 constrained only by residue coevolution can recover the binding interface
 of atomic X-ray dimer complexes with remarkable accuracy (ca. 1 Å RMSD).
 We propose a model for FliM-FliN heterodimerization, which agrees
 accurately with homologous interfaces as well as in-situ cross-linking
 experiments, and hence supports a proposed architecture for the lower
 portion of the C-ring. Furthermore, this approach allowed the
 identification of two discrete and interchangeable homodimerization
 interfaces between FliM middle domains that agree with experimental
 measurements and might be associated with C-ring directional switching
 dynamics triggered upon binding of CheY signal protein. Our findings
 provide structural details of complex formation at the C-ring that have
 been difficult to obtain with previous methodologies and clarify the
 architectural principle that underpins the ultra-sensitive allostery
 exhibited by this ring assembly that controls the clockwise (CW) or
 counterclockwise (CCW) rotation of flagella.
description: Chemical Cross-Links in
 FliM homodimerizationChemical Cross-links
 reported in literature and used to support the predicted models for FliM
 middle domain homodimerization.cross_linking_FliMm_allMSA of FliM middle domain familymultiple sequence alignment used to compute coevolution signals in the middle domain of FliM protein from T. maritmaFLIM_Thermotoga_maritma_filter30gap.afaMSA for FliM/N c-terminal familyMultiple Sequence Alignment used to compute coevolution signals in FliN C-terminal and FliM C-terminal domains. These couplings were mapped to predict FliN C-terminal homodimerization in validation process and to predict a model for FliN/FliM C-terminal heterodimerization.FliMNcterminal_PF01052_uniprot_format.afaPrediction of FliN C-terminal homodimerPrediction of FliN C-terminal homodimer through simulations with structure-based models driven by coevolution signals. The final model presented a RMSD of 0.81Å when compared to experimental X-ray structure (1O6A). This prediction was used as a validation step to support subsequent models.FliN_homodimer_predicted.pdbprediction of FliNM heterodimerizationPrediction of FliN/FliM C-terminal heterodimer through simulations with structure-based models driven by coevolution signals.FliNM_heterodimer_predicted.pdbpredicted FliM homodimer model IPredicted homodimerization interface of FliM middle domain in a parallel configuration that is compatible to the interaction mode of one rotational state suggested by cryo-EM data fitting and chemical cross-linking experiments.FliM_homodimer_cluster1.pdbpredicted FliM homodimer model IIPredicted homodimerization interface of FliM middle domain in a twisted configuration that is supported by chemical cross-linking experiments and can be related to an alternative conformational state of flagellum rotation.FliM_homodimer_cluster2.pdbRecurring Chemical Cross-Links in FliN/FliM C-terminal homodimerizationChemical Cross-Links in FliN/FliM C-terminal dimerization that are present in both rotational states of flagellar motor. This dataset from literature was used to support predicted model for FliN/FliM C-terminal heterodimer.both_modesChemical Cross-Links observed in the CW state of FliN/FliM C-terminal dimerChemical Cross-Links in FliN/FliM C-terminal dimerization that are observed only in CW rotational states of flagellar motor. This dataset from literature was used to support predicted model for FliN/FliM C-terminal heterodimer.CW_modeChemical Cross-Links observed in the CCW state of FliN/FliM C-terminal dimerChemical Cross-Links in FliN/FliM C-terminal dimerization that are observed only in CCW rotational states of flagellar motor. This dataset from literature was used to support predicted model for FliN/FliM C-terminal heterodimer.CCW_modeDCA for FliM modelsCoevolution couplings derived from Direct-Coupling Analysis used to predict FliM middle domain homodimers (parallel and twisted models).DCA_FliM_middleDCA for FliM/FliN modelCoevolution couplings derived from Direct-Coupling Analysis used to predict the dimerization interface of FliM/FliN C-terminal domain.DCA_FliN_FliM_CterminalDCA for FliN homodimer modelCoevolution couplings derived from Direct-Coupling Analysis used to predict the dimerization interface of FliN C-terminal domain (validation of methodology).DCA_FliN_Cterminal