On 2016 Oct 27, Andy Collings commented:

Jawdat Al-Bassam's comment on this article (https://elifesciences.org/content/4/e08811#comment-2953448767) is reproduced below:

Negative stain EM 3D-reconstruction and consequent interpretations are often ambiguous due to their low resolution and rely on biochemical data for substantiation as provided in our manuscript. During the past year, we have used different 3D-reconstruction strategies to re-analyze negative stain data and obtain structures. From this re-analysis, we observed some changes in the features of 3D-reconstructions in Figures 5 and 7 in a program-dependent manner, which could result in changes to the fitted models described in Figures 5 and 7. As such, we would like the community to be aware that there are possible ambiguities and alternative interpretations of the published reconstructions, which likely arose from complex heterogeneity due to different conformational states or deformations from the negative staining process. However, these potential reconstruction differences do not change the general conclusions made in the manuscript regarding the overall organization of the complexes and the sites of binding for tubulin and tubulin cofactor C at low resolution. In addition, we deposited our raw data several months ago (EMPAIR-10034, 10035) and welcome suggestions and input from the community. We are currently focused on high-resolution structural studies using cryo-electron microscopy that will allow us to determine the de novo structure for the Tubulin cofactors-D-E with Arl2 assembly in complex with Tubulin dimer and Tubulin cofactor C.

Jawdat Al-Bassam (jawdat@ucdavis.edu)

On 2016 Oct 27, Andy Collings commented:

Jawdat Al-Bassam's comment on this article (https://elifesciences.org/content/4/e08811#comment-2953448767) is reproduced below:

Negative stain EM 3D-reconstruction and consequent interpretations are often ambiguous due to their low resolution and rely on biochemical data for substantiation as provided in our manuscript. During the past year, we have used different 3D-reconstruction strategies to re-analyze negative stain data and obtain structures. From this re-analysis, we observed some changes in the features of 3D-reconstructions in Figures 5 and 7 in a program-dependent manner, which could result in changes to the fitted models described in Figures 5 and 7. As such, we would like the community to be aware that there are possible ambiguities and alternative interpretations of the published reconstructions, which likely arose from complex heterogeneity due to different conformational states or deformations from the negative staining process. However, these potential reconstruction differences do not change the general conclusions made in the manuscript regarding the overall organization of the complexes and the sites of binding for tubulin and tubulin cofactor C at low resolution. In addition, we deposited our raw data several months ago (EMPAIR-10034, 10035) and welcome suggestions and input from the community. We are currently focused on high-resolution structural studies using cryo-electron microscopy that will allow us to determine the de novo structure for the Tubulin cofactors-D-E with Arl2 assembly in complex with Tubulin dimer and Tubulin cofactor C.

Jawdat Al-Bassam (jawdat@ucdavis.edu)