[6] Li Y, Zhou Y, Yuan J, et al. CryoSTAR: leveraging structural priors and constraints for cryo-EM heterogeneous reconstruction [J]. Nature Methods, 2024: 1-9. [7] Zhou Y, Li Y, Yuan J, et al. CryoFM: A Flow-based Foundation Model for Cryo-EM Densities. arXiv preprint arXiv:...
Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have ...
(Fig.5hand Extended Data Figs.9c,f,10). To our knowledge this is a high resolution achieved by cryo-EM for this size of protein4,6,7,38,39,40. Streptavidin is composed of four monomers, the densities of which were clearly resolved on the 2.2 Å map (Fig.5h). Furthermore, ...
Caution was taken not to mask out the densities for the bound ligand and lipids. The map was then extended by 2 pixels and supplied with a soft edge width of 12 pixels using relion_mask_create. g, Local-resolution map for the 3D EM reconstruction of Cav3.1-Δ8b in the presence of Z...
In the case of both Morhphology-1a and 1b, extra densities were observed near the contact sites of two protofilaments (Supplementary Fig. 3b). At the current resolution of the 3D maps, we cannot comment on the origin of these extra densities. However, it can be possible that they arise...
We did not resolve densities in our structures that can be interpreted as bound PIP2. However, our earlier studies showed that the N-terminal segment bearing a cluster of positively charged residues is crucial for PIP2 modulation of TMEM16F channel activity (Ye et al., 2018). In our structu...
Densities are shown as a semi-transparent surface following a similar colour scheme to that in the main section. A region corresponding to the double-psi beta-barrel domain composing the conserved core of Pol II within Rpb1 and Rpb2 is shown as an example of near-atomic resolution features....
Central cross-section of the cryo-EM map showing the Fab densities (blue). The enlarged inset shows the density corresponding to one Fab AT12-015 molecule. The V and V domains represented by green and blue ribbons are well defined in the density map. The six complementarity-determining ...
For accuracy of fits, besides the final maps filtered to ∼7.1 Å, also maps filtered to 4.5 Å were used (based on the ResMap-determined local resolution), which displayed density features along helical densities in local higher-resolution regions for larger side chains, such as tyrosines...
The cryo-EM densities of the RP–CP interfaces are shown as a grey surface representation. The red dashed circles highlight the densities of the RPT C-terminal tails. b, Close-up views and comparison of the RPT C-tail densities superimposed with the atomic models in different states. The ...