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. 2012 Dec 5;20(12):2003-13.
doi: 10.1016/j.str.2012.10.016.

Protein secondary structure determination by constrained single-particle cryo-electron tomography

Alberto Bartesaghi  1 , Federico Lecumberry, Guillermo Sapiro, Sriram Subramaniam
Affiliations

Protein secondary structure determination by constrained single-particle cryo-electron tomography

Alberto Bartesaghi et al. Structure. .

Abstract

Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series.

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Figures

Figure 1
Figure 1. Conceptual Foundation of Constrained Single-Particle Tomography Refinement
Imaging single-particles using cryo-ET imposes geometric constraints between particle projections that can be enforced in the refinement of image orientations. (A) Imaging Pi=1:3 single-particles using a series of tilted projections produces a set of micrographs Mi=1:3, each at a different tilt angle. Individual particle projections Ii=1:9 are then extracted and subjected to refinement to determine their relative orientations in 3D. (B) Particle projections can be arranged into a 2D matrix where each column represents projections of the same single-particle Pi, and each row represents projections extracted from the same micrograph Mi. Constrained refinement of particle orientations guarantees that the angular relationship between projections of the same single-particle does not change during refinement (red lock). Likewise, refinement of parameters of the tilt geometry guarantees their coplanarity constraint throughout the refinement procedure (blue lock).
Figure 2
Figure 2. CTF Correction and Identification of Best Quality Images from Tilt Series of GroEL
Tilt series of GroEL were collected and processed using conventional subvolume averaging (see Experimental Procedures) and the proposed reconstruction strategy. (A) Zero-tilt exposure from representative tilt series at ~2.3 e−/Å2. (B) Slice through corresponding tomographic reconstruction (~105 e−/Å2 accumulated dose). Scale bars, 35 nm. (C) Theoretical CTF curve at 2.5 μm defocus estimated from radially averaged, background-subtracted, 1D power spectrum obtained by periodogram averaging using tiles from the tilt series. (D) FSC against X-ray model of GroEL of non-CTF corrected conventional subvolume averaging reconstruction from 10,000 GroEL particles and proposed CTF-corrected reconstruction by merging of projection sets. (E and F) Difference in image quality between successive exposures in the tilt series and its impact on resolution of reconstructions. (E) Average phase residual per exposure in the tilt series plotted as a function of the tilt angle using a two-branch data collection scheme (0° to −45° and 2° to 45°). (F) FSC of reconstructions using first 11 exposures from first branch (0° to −20°) and first ten exposures from second branch (2° to 20°). See also Figure S1.
Figure 3
Figure 3. Constrained Refinement Minimizes Overfitting Effects and Produces Subnanometer Resolution Structures from Low-Dose Tomographic Tilt Series of GroEL
Using particle projections extracted from the tilt series of GroEL, we compared the performance of orientation-fixed, traditional, and constrained projection-matching refinement in terms of agreement of assigned orientations with the tomographic constraints, value of the projection-matching objective function and resolution of reconstructions. (A–C) Amplitude-corrected reconstructions obtained using orientation-fixed, traditional, and constrained projection-matching refinement, respectively. (D) Comparison of orientations assigned to projections of the same single-particle by the three refinement strategies represented on the asymmetric triangle. (E) Tracking of the projection matching objective function represented by Equation (1) for each of the three refinement strategies as a function of refinement iteration. (F) FSC plots of reconstructions shown in (A)–(C) against X-ray model of GroEL. Color code in (D)–(F) is the same as in (A)–(C).
Figure 4
Figure 4. Progressive Improvement in Resolution Achieved by Each Component of Constrained Single-Particle Tomography and Comparison to Highest Resolution Map of GroEL Reported Using Cryo-EM
Maps are represented as iso-surfaces with the fitted X-ray coordinates. (A) Reconstruction by conventional subvolume averaging. (B–D) Fourier-based CTF-corrected reconstructions using only first 11 exposures in the tilt series and alignments from subvolume averaging (B), after traditional projection-matching refinement of image shifts (C), and after constrained projection-matching refinement (D). (E) FSC plots of maps in (A)–(D) obtained from the correlation of reconstructions between random halves of the image data set, indicating resolutions measured by the 0.5 cutoff criteria of 24.5, 15.3, 10.6, and 8.4 Å, respectively. (F) FSC plots against a map derived from the X-ray model indicating resolutions measured by the 0.5 cutoff criteria of 34.1, 18.2, 10.8, and 8.5 Å for maps in (A)–(D) and 8.2 Å for map shown in (K). (G–J) Maps of the entire complex corresponding to the subunits shown in (A)–(D). (K) Map (4.2 Å) of GroEL (EMDB ID 5001) obtained by traditional single-particle cryo-EM (Ludtke et al., 2008), using 20,401 particles, 25–36 e−/Å2 and 300 kV imaging (iso-surface shown at suggested contour level of 0.597).
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