Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Construction of atomic models of the 54mers using 18mers

FS Franziska L. Sendker
YL Yat Kei Lo
TH Thomas Heimerl
SB Stefan Bohn
LP Louise J. Persson
CM Christopher-Nils Mais
WS Wiktoria Sadowska
NP Nicole Paczia
EN Eva Nußbaum
MO María del Carmen Sánchez Olmos
KF Karl Forchhammer
DS Daniel Schindler
TE Tobias J. Erb
JB Justin L. P. Benesch
EM Erik G. Marklund
GB Gert Bange
JS Jan M. Schuller
GH Georg K. A. Hochberg
request Request a Protocol
ask Ask a question
Favorite

We used the align, translate, and rotate commands within PyMOL (v.2.5.2) to model how a 54mer complex would assemble if the 4.0° and 4.2° dimer rotations and 60° dihedral angle between dimers that are observed in the 18mer structure were applied. The rotation was applied to the connecting dimers of the three 18mer-subcomplexes that built the 54mer. To do this, copies of the hexamers that constitute the 18mer were rotated by 120°, so as to overlay the corner dimers by edge dimers. Two 18mer copies were subsequently connected to the rotated corners by two steps of structural alignment, which placed the residues that should form the third interface 210 Å from each other (Extended Data Fig. ​Fig.2g2g).

Copyright and License information: The Author(s) ©2024
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A