English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

Subramaniam (1), van Heel (2), and Henderson (3) express their opinions and hypotheses about our cryo-electron microscopy (EM) structures of the uncleaved HIV-1 envelope glycoprotein [Env(-)ΔCT] trimer (4, 5). There are no data in these communications, nor elsewhere in the published literature, that contradict our results; however, we conducted systematic additional studies that provide strong evidence disproving their hypotheses. We appreciate the potential pitfalls of analyzing low-contrast images and indeed took specific measures to avoid reference bias in our particle-picking approach (6). Importantly, we conducted validation studies on our Env(-)ΔCT structures using independent datasets and tests. We offered the primary data to the reviewers of this communication. We respond to the comments of Subramaniam, van Heel, and Henderson as follows. In single-particle cryo-EM, a tradeoff exists between the contrast of the specimen image and the achievable resolution (7). To allow determination of the Env(-)ΔCT structure at optimal resolution, a large number of closer-to-focus, low-contrast images from focal pairs were analyzed. The signal-to-noise ratio (SNR) of our particles is comparable to those used in other cryo-EM studies that sought to maximize resolution; we deposited a set of original micrographs in the Electron Microscopy Data Bank to allow investigators to evaluate the raw data (8). Subramaniam’s and Henderson’s comparisons of our dose-limited micrographs with their overdosed particle images (1, 3) are misleading; to achieve high contrast in their examples, high-resolution information in those overdosed images is sacrificed as a result of excessive radiation damage. We devised an approach to select and validate particles from low-contrast images that is sensitive, yet avoids reference bias from the particle-picking template (6). In this dual-target function validation approach, fast local correlation with a low-resolution template was used for automated particle picking (9), followed by particle verification through maximum-likelihood (ML) image alignment (10, 11 …

Reply to Subramaniam, van Heel, and Henderson: Validity of the cryo-electron microscopy structures of the HIV-1 envelope glycoprotein complex