Homology model of the C-terminal domain of human annexin A11 (ANXA11) based on human annexin A4

This archive contains generation files and homology models of human annexin A11’s C-terminal domain (residues 192-505) with or without 4 bound calcium ions, built using human annexin A4 with bound calcium.

Representative models

A single representative model was selected for the apo: anxa11_cterm.B99990009.pdb
A single representative model was selected for the holo protein: anxa11_cterm.B999900038.pdb
 

Methods

The template coordinates of chain A were extracted from PDB ID 2ZOC. The alignment contains no gaps, as indicated by iTasser. In the holo model, distance restraints between calcium ions and nearby oxygen atoms were assigned based on the equivalent distances in the template, as computed using PyMol. The final model was selected from the attached ensemble of 100 models in the *all_100_models* folder. Models were generated by Modeller 9.20 with the input files in the *Modeller_files/* subfolder, before filtration with MolPDF, then ProQ, then PROCHECK, then MolProbity.

Electrostatic surfaces were shown using the files in the *Electrostatics/* subfolder. The calcium atoms were renamed using *rename_cal.csh*, and the resultant pdb file *anxa11_cterm.B99990038_rename.pdb* was used as input to generate the correct partial charges using APBS v1.3 with the CHARMM force field. The maps of the calcium-free model were generated for the pdb file *anxa11_cterm.B99990009.pdb*. This assumes no major conformational changes occur as a result of calcium binding, which is likely to be the case, based on comparison of calcium-bound 2ZOC and calcium-free 2ZHJ. The pymol session containing the maps can be viewed with Pymol v2.3.0

This work was supported by the National Institutes of Health, National Institute of Neurological Disorders and Stroke intramural research program.

For more details, see Liao Y-C, Fernandopulle M, Wang G, Choi H, Hao L, Drerup CM, Qamar S, Nixon-Abel J, Shen Y, Meadows W, Vendruscolo M, Knowles T, Nelson M, Czekalska M, Musteikyte G, Gachechiladze M, Patel R, Stephens C, Pasolli A, Forrest LR, St George-Hyslop P, Lippincott-Schwartz J, Ward ME, "RNA granules hitchhike on lysosomes for long-distance transport, using annexin A11 as a molecular tether" Cell (2019) in press.