Simulation and structural modelling data files for "TBK1 restricts IRGQ-mediated autophagy"

Raw Data files for Modeling and Simulations of IRGQ-GBRL2 Complexes * Data corresponding to the study: TBK1 restricts IRGQ-mediated autophagy DOI: https://doi.org/10.64898/2026.01.07.698103 (bioRxiv) * Authors of publication: Gestal-Mato, Uxia (0000-0002-6004-7420) 1 Lascaux, Pauline (0000-0003-3935-6795) 1 Poveda Cuevas, Sergio Alejandro (0000-0002-3087-6674) 1, 2, ++ Cristiani, Alberto (0009-0004-8273-3386) 1, 2, ++ Camp, Belinda (0009-0007-3633-2356) 3 Aghapour, Mahyar (0000-0002-3548-3423) 3 Viswanathan Ammanath, Aparna (0000-0001-9602-3757) 1 Bhaskara, Ramachandra M. (0000-0002-7742-0391) 1, 2, ++ Dikic, Ivan (0000-0001-8156-9511) 1, 2, 4 Herhaus, Lina (0000-0001-6198-227X) 1, 3 ++ To whom correspondence should be addressed to E-mail: [e-mail] (S.A.P.C.), [e-mail] (A.C.), and [e-mail] (R.M.B.) * Affiliations/Addresses: 1. Goethe University Frankfurt, Institute of Biochemistry II, University Hospital Building 75, Theodor-Stern-Kai 7, 60590 Frankfurt (Main), Germany2. Buchmann Institute for Molecular Life Sciences, Riedberg Campus, Max-von-Laue-Str. 15, 60438 Frankfurt (Main), Germany3. Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany4. Max Planck Institute of Biophysics, Goethe University Frankfurt, Riedberg Campus, 60438 Frankfurt am Main, Germany * Description: - Fig_S1_S4_S5.xlsx -> Summary table with data for all figures (S1, S4, S5) 1. Fig. S1C -> AlphaFold2 multimer models (ensemble of 100 PDB models converted to .xtc format) - reference_run1_irgq-gbrl2.pdb + ensemble_run1_irgq-gbrl2.xtc -> multimer complex IRGQ-GABARAPL2 2. Fig. S4B -> Representative raw trajectory files (.xtc) with input configuration (.gro) and PDB files from atomistic MD simulations (GROMACS 2021, 3 replicates x 1000 ns) for: - wt_irgq_1-189_vs_gabarapl2 -> IRGQ(1-189)-GBRL2(WT): truncated IRGQ in complex with GBRL2 Files: proteins_nH.pdb + trajectory_dt_1000.xtc - s10p_irgq_1-189_vs_gabarapl2 -> IRGQ(1-189)-GBRL2(S10PO4): truncated IRGQ in complex with GBRL2 (Phosphorylated on Ser10) Files: proteins_nH.pdb + trajectory_dt_1000.xtc 3. Fig. S4E -> Representative raw trajectory files (.xtc) and PDB files from coarse-grained Go-Martini 3.0 simulations of full-length IRGQ in complex with GBRL2 (WT) Files: proteins.pdb + trajectory_dt1000.xtc 4. Fig. S4F -> Representative raw trajectory files (.xtc) and PDB files from coarse-grained Go-Martini 3.0 simulations of full-length IRGQ in complex with GBRL2 (S10D phosphomimetic) Files: proteins.pdb + trajectory_dt1000.xtc 5. Fig. S5A -> AlphaFold2 multimer models (ensemble of 100 PDB models converted to .xtc format) - reference_run2_irgq-gbrl2-atg7.pdb + ensemble_run2_irgq-gbrl2-atg7.xtc -> multimer complex IRGQ-GABARAPL2-ATG7 6. Fig. S5B -> AlphaFold2 multimer models (ensemble of 100 PDB models converted to .xtc format) - reference_run3_irgq-gbrl2-lc3b-atg7.pdb + ensemble_run3_irgq-gbrl2-lc3b-atg7.xtc -> multimer complex IRGQ-GABARAPL2-LC3B-ATG7 For further details check: https://doi.org/10.64898/2026.01.07.698103 (bioRxiv). * Summary of content ├── Fig_S1_S4_S5.xlsx├── Fig. S1C│ ├── ensemble_run1_irgq-gbrl2.xtc│ └── reference_run1_irgq-gbrl2.pdb├── Fig. S4B│ ├── s10p_irgq_1-189_vs_gabarapl2│ │ ├── proteins_nH.pdb│ │ └── trajectory_dt_1000.xtc│ └── wt_irgq_1-189_vs_gabarapl2│ ├── proteins_nH.pdb│ └── trajectory_dt_1000.xtc├── Fig. S4E│ ├── proteins.pdb│ └── trajectory_dt1000.xtc├── Fig. S4F│ ├── proteins.pdb│ └── trajectory_dt1000.xtc├── Fig. S5A│ ├── ensemble_run2_irgq-gbrl2-atg7.xtc│ └── reference_run2_irgq-gbrl2-atg7.pdb├── Fig. S5B│ ├── ensemble_run3_irgq-gbrl2-lc3b-atg7.xtc│ └── reference_run3_irgq-gbrl2-lc3b-atg7.pdb└── README.txt