De Novo Protein Structure Determination from Near-atomic-resolution Cryo-EM Maps

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2015 Feb 24

PMID 25707029

Citations 109

Authors

Ray Yu-Ruei Wang

Mikhail Kudryashev

Xueming Li

Edward H Egelman

Marek Basler

Yifan Cheng

David Baker

Frank DiMaio

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Octahedral small virus-like particles of dengue virus type 2.

Johnson A, Dodes Traian M, Walsh Jr R, Jenni S, Harrison S J Virol. 2025; 99(2):e0180924.

PMID: 39745459 PMC: 11853069. DOI: 10.1128/jvi.01809-24.

The big chill: Growth of structural biology with cryo-electron tomography.

Kudryashev M QRB Discov. 2024; 5:e10.

PMID: 39687233 PMC: 11649376. DOI: 10.1017/qrd.2024.10.

Automated detection and de novo structure modeling of nucleic acids from cryo-EM maps.

Li T, Cao H, He J, Huang S Nat Commun. 2024; 15(1):9367.

PMID: 39477926 PMC: 11525807. DOI: 10.1038/s41467-024-53721-4.

Fast In Vitro Synthesis and Direct Labeling of Nanobodies for Prototyping in Microscopy Applications.

Behrens L, Walter R, Cai W, Ewers H, van Bommel B, Zemella A ACS Omega. 2024; 9(33):35374-35383.

PMID: 39184460 PMC: 11339826. DOI: 10.1021/acsomega.4c01164.

Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L.

Benoit M, Rao L, Asenjo A, Gennerich A, Sosa H Nat Commun. 2024; 15(1):5530.

PMID: 38956021 PMC: 11219953. DOI: 10.1038/s41467-024-48720-4.

References

Amunts A, Brown A, Bai X, Llacer J, Hussain T, Emsley P . Structure of the yeast mitochondrial large ribosomal subunit. Science. 2014; 343(6178):1485-1489. PMC: 4046073. DOI: 10.1126/science.1249410. View

Veesler D, Ng T, Sendamarai A, Eilers B, Lawrence C, Lok S . Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography. Proc Natl Acad Sci U S A. 2013; 110(14):5504-9. PMC: 3619359. DOI: 10.1073/pnas.1300601110. View

Bradley P, Misura K, Baker D . Toward high-resolution de novo structure prediction for small proteins. Science. 2005; 309(5742):1868-71. DOI: 10.1126/science.1113801. View

Wriggers W, Milligan R, McCammon J . Situs: A package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol. 1999; 125(2-3):185-95. DOI: 10.1006/jsbi.1998.4080. View

Rosenthal P, Henderson R . Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol. 2003; 333(4):721-45. DOI: 10.1016/j.jmb.2003.07.013. View

Terwilliger T, Grosse-Kunstleve R, Afonine P, Moriarty N, Zwart P, Hung L . Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Crystallogr D Biol Crystallogr. 2007; 64(Pt 1):61-9. PMC: 2394820. DOI: 10.1107/S090744490705024X. View

Rossmann M, Bernal R, Pletnev S . Combining electron microscopic with x-ray crystallographic structures. J Struct Biol. 2002; 136(3):190-200. DOI: 10.1006/jsbi.2002.4435. View

Zhang X, Settembre E, Xu C, Dormitzer P, Bellamy R, Harrison S . Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc Natl Acad Sci U S A. 2008; 105(6):1867-72. PMC: 2542862. DOI: 10.1073/pnas.0711623105. View

DiMaio F, Song Y, Li X, Brunner M, Xu C, Conticello V . Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nat Methods. 2015; 12(4):361-365. PMC: 4382417. DOI: 10.1038/nmeth.3286. View

10.

Lindert S, Staritzbichler R, Wotzel N, Karakas M, Stewart P, Meiler J . EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure. 2009; 17(7):990-1003. PMC: 3760413. DOI: 10.1016/j.str.2009.06.001. View

11.

Cowtan K . The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr D Biol Crystallogr. 2006; 62(Pt 9):1002-11. DOI: 10.1107/S0907444906022116. View

12.

DiMaio F, Tyka M, Baker M, Chiu W, Baker D . Refinement of protein structures into low-resolution density maps using rosetta. J Mol Biol. 2009; 392(1):181-90. PMC: 3899897. DOI: 10.1016/j.jmb.2009.07.008. View

13.

Li X, Mooney P, Zheng S, Booth C, Braunfeld M, Gubbens S . Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods. 2013; 10(6):584-90. PMC: 3684049. DOI: 10.1038/nmeth.2472. View

14.

Roseman A . FindEM--a fast, efficient program for automatic selection of particles from electron micrographs. J Struct Biol. 2004; 145(1-2):91-9. DOI: 10.1016/j.jsb.2003.11.007. View

15.

DiMaio F, Soni A, Phillips Jr G, Shavlik J . Spherical-harmonic decomposition for molecular recognition in electron-density maps. Int J Data Min Bioinform. 2009; 3(2):205-27. PMC: 2696052. DOI: 10.1504/ijdmb.2009.024852. View

16.

Trabuco L, Villa E, Mitra K, Frank J, Schulten K . Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure. 2008; 16(5):673-83. PMC: 2430731. DOI: 10.1016/j.str.2008.03.005. View

17.

Song Y, DiMaio F, Wang R, Kim D, Miles C, Brunette T . High-resolution comparative modeling with RosettaCM. Structure. 2013; 21(10):1735-42. PMC: 3811137. DOI: 10.1016/j.str.2013.08.005. View

18.

Hryc C, Chen D, Chiu W . Near-atomic-resolution cryo-EM for molecular virology. Curr Opin Virol. 2011; 1(2):110-7. PMC: 3155204. DOI: 10.1016/j.coviro.2011.05.019. View

19.

Allegretti M, Mills D, McMullan G, Kuhlbrandt W, Vonck J . Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. Elife. 2014; 3:e01963. PMC: 3930138. DOI: 10.7554/eLife.01963. View

20.

Lange O, Baker D . Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins. 2012; 80(3):884-95. PMC: 3310173. DOI: 10.1002/prot.23245. View