DOI: 10.5061/dryad.69p8cz957
title: Molecular models of the FtsQ-FtsL-FtsB-FtsW-FtsI complex (FtsQLBWI) in mono- and diprotomeric configurations

description: The data consists of five Protein Data Bank (PDB) structure files of the
 complex formed by FtsQ, FtsL, FtsB, FtsW, and FtsI of the divisome of
 Escherichia coli (FtsQLBWI).  The five PDB files consist of an
 original AlphaFold2 model, partially validated through mutagenesis in
 vivo, and a series of derivatives remodeled seeking insight into the
 potential structural transitions that lead to activation of the FtsWI
 complex, which produced peptidoglycan during cell division. In the
 original model (file FtsQLBWI_protomer_original.pdb), FtsLB serves as a
 support for FtsI, placing its periplasmic domain in an extended and
 possibly active conformation.  We remodeled the periplasmic
 domain of FtsI to assess it the model is compatible with a compact and
 possibly inactive conformation (file FtsQLBWI_protomer_compact.pdb).
 Additionally, the complex was remodeled to assume an Fts[QLBWI]2
 diprotomeric configuration, using FtsLB as a central hub (file
 FtsQLBWI_diprotomer_clashing.pdb).  This was performed by
 applying the C2 symmetry operation (180° rotation) to the Fts[QLBWI]1
 complex that reconstructs the Fts[LB]2 complex in the Y-model
 configuration from the Fts[LB]1 AlphaFold2 prediction.  In this
 model, a severe steric overlap occurs between FtsQ and FtsI, which occupy
 the same region of space adjacent to FtsLB. To address whether this clash
 could be solved by providing flexibility to a hinge in the CCD region of
 FtsLB, we used a procedure, based on docking of FtsQ with HADDOCK followed
 by loop reconstruction with Rosetta (file
 FtsQLBWI_diprotomer_extended.pdb). Finally, we reconfigured the initial
 diprotomeric model in a compact state (file
 FtsQLBWI_diprotomer_compact.pdb).
description: The original data was obtained by submitting the sequences of
 FtsQ, FtsL, FtsB, FtsW, and FtsI to AlphaFold2 (ColaFold) (1). The
 monoprotomeric FtsQLBWI complex was reconfigured using homology modeling
 using the SWISS-MODEL webserver (2). The reconfiguration in a diprotomeric
 configuration was performed using a program written with MSL (3).
 Remodeling of FtsQ in the diprotomeric extended state was performed with
 HADDOCK (4) and Rosetta (5). References:
 1. Mirdita M, Ovchinnikov S, Steinegger M. ColabFold - Making
 protein folding accessible to all [Internet]. Bioinformatics; 2021 Aug
 [cited 2021 Sep 14]. 2. Waterhouse A, Bertoni M,
 Bienert S, Studer G, Tauriello G, Gumienny R, et al. SWISS-MODEL: homology
 modelling of protein structures and complexes. Nucleic Acids Res. 2018 Jul
 2;46(W1):W296–303. 3. Kulp DW, Subramaniam S, Donald
 JE, Hannigan BT, Mueller BK, Grigoryan G, et al. Structural informatics,
 modeling, and design with an open-source Molecular Software Library (MSL).
 J Comput Chem. 2012 Jul 30;33(20):1645–61. 4. Dominguez
 C, Boelens R, Bonvin AMJJ. HADDOCK: A Protein−Protein Docking Approach
 Based on Biochemical or Biophysical Information. J Am Chem Soc. 2003 Feb
 19;125(7):1731–7. 5. Huang PS, Ban YEA, Richter F,
 Andre I, Vernon R, Schief WR, et al. RosettaRemodel: A Generalized
 Framework for Flexible Backbone Protein Design. Uversky VN, editor. PLoS
 ONE. 2011 Aug 31;6(8):e24109.
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