EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies

Abstract

Structural analysis of biological machines is essential for inferring their function and mechanism. Nevertheless, owing to their large size and instability, deciphering the atomic structure of macromolecular assemblies is still considered as a challenging task that cannot keep up with the rapid advances in the protein-identification process. In contrast, structural data at lower resolution is becoming more and more available owing to recent advances in cryo-electron microscopy (cryo-EM) techniques. Once a cryo-EM map is acquired, one of the basic questions asked is what are the folds of the components in the assembly and what is their configuration. Here, a novel knowledge-based computational method, named EMatch, towards tackling this task for cryo-EM maps at 6-10 A resolution is presented. The method recognizes and locates possible atomic resolution structural homologues of protein domains in the assembly. The strengths of EMatch are demonstrated on a cryo-EM map of native GroEL at 6 A resolution.

Figure 1

EMatch flow. The strategy of EMatch consists of three stages. In the first stage, helices are identified in a given cryo-EM map of a protein complex. Their spatial arrangement is then used to query a data set of atomic resolution folds to find potential structural homologues of domains appearing in the map. In the final stage, which is currently under development, the potential atomic structural homologues of the domains are assembled into a quasi-model of the complex.

Figure 2

A priori known domain reconstruction. (a–c) The matched helices of the top-ranking alignment for the intermediate (blue), equatorial (red) and apical (yellow) domains, respectively. (d) A quasi-atomic structural model of a GroEL ring as revealed from the cryo-EM map (depicted in grey). This figure and subsequent figures were prepared using Chimera (Pettersen et al., 2004 ▶).

Figure 3

Evaluation of a priori known domain reconstruction. (a) A quasi-atomic structural model of a GroEL ring (coloured as in Fig. 2 ▶) superimposed on its X-­ray crystal structure (PDB code 1oel; grey) with a minimum r.m.s.d. of 5.17 Å. (b–d) Enlargement of the superimposed apical, equatorial and intermediate domains, respectively.

Figure 4

Evaluation of a priori unknown domain reconstruction. (a) The SCOP superfamily representative for the equatorial domain (red) superimposed by EMatch on the cryo-EM map (not shown) and the same structure (grey) superimposed by MASS on the atomic quasi-structural model constructed in the first experiment. (b) and (c) Similar figures for the apical (yellow) and intermediate (blue) domains, respectively.