De novo protein structure determination from near-atomic resolution cryo-EM maps

By R. Wang, M. Kudryashev, Xueming Li, Edward H. Egelman, Marek Basler, Yifan Cheng, David Baker, Frank DiMaio. 2015

188 citations recorded by the source corpus.

We present a de novo model-building approach that combines predicted backbone conformations with side-chain fit to density to accurately assign sequence into density maps. This method yielded accurate models for six of nine experimental maps at 3.3- to 4.8-Å resolution and produced a nearly complete model for an unsolved map containing a 660-residue heterodimeric protein. This method should enable rapid and reliable protein structure determination from near-atomic-resolution cryo-electron microscopy (cryo-EM) maps.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Jeffrey J. Gray
2. Frank DiMaio
3. Jens Meiler
4. David Baker
5. Tom Burnley
6. S. W. Hoh
7. Sergey Lyskov
8. Rhiju Das

In Molecular Biology

1. Jeffrey J. Gray
2. Jens Meiler
3. David Baker
4. Frank DiMaio
5. Sergey Lyskov
6. Rhiju Das
7. Tom Burnley
8. S. W. Hoh

In Structural Biology

1. S. W. Hoh
2. Tom Burnley
3. Kevin Cowtan
4. Yifan Cheng
5. Frank DiMaio
6. James S. Fraser
7. Yifan Song
8. Benjamin A. Barad

Citations in the corpus

• Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta (2016, background): “Cryo-EM reconstructions at these resolutions, where individual β-strands are resolvable, and bulky sidechains are somewhat visible, make it possible to build an all-atom model directly from such maps [4,5].”
• Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE) (2018, background): “…interactions, 5,6 and protein–small molecule interactions, 7,8 to the use of nuclear magnetic resonance 9,10 and electron density information 11,12 in structure prediction and refinement, to the design of novel protein folds, 13,14 protein–protein interactions, 15,16 protein– small molecule…”
• Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM (2020, methodology): “…of existing and the development of new model-building tools to interpret cryo-EM maps (Cowtan, 2008; Baker et al., 2012; Brown et al., 2015; Wang et al., 2015; Chen et al., 2016; Zhou et al., 2017; Terwilliger, Adams et al., 2018; Terashi & Kihara, 2018; Afonine, Poon et al., 2018;…”