Metabolic enzyme beta-galactosidase at high resolution

2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor

Alberto Bartesaghi1,Alan Merk1,*,Soojay Banerjee1,Doreen Matthies1,Xiongwu Wu2,Jacqueline L. S. Milne1,Sriram Subramaniam1,

Science 5 June 2015:
Vol. 348 no. 6239 pp. 1147-1151
DOI: 10.1126/science.aab1576

Figure 1.  EMDB EMD-2984  Imported into Sketchfab

Abstract:

Cryo–electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM.

EMD 2984 & PDB 5A1A

Figure 2.  EMDB EMD-2984 and PDB 5A1  Imported into Sketchfab

Read Science Editor’s Summary of this work (Science, this issue p. 1147:

Pushing the limits of electron microscopy

Recent advances in cryo–electron microscopy (cryo-EM) allow structures of large macromolecules to be determined at near-atomic resolution. So far, though, resolutions approaching 2 Å, where features key to drug design are revealed, remain the province of x-ray crystallography. Bartesaghi et al. achieved a resolution of 2.2 Å for a 465-kD ligand-bound protein complex using cryo-EM. The density map is detailed enough to show close to 800 water molecules, magnesium and sodium ions, and precise side-chain conformations. These results bring routine use of cryo-EM in rational drug design a step closer.

Science, this issue p. 1147

 

 

Cryo-electron microscopy (3DEM) data into  Sketchfab

(EMD-2984) was downloaded from the EMDataBank and imported into Chimera.  EMD-2984 and PDB 5A1A were exported from Chimera in .obj format.  In 3DS Max, the surface corresponding to each beta galactosidase subunit was selected and assigned a color channel.   The model was exported from 3DS Max in either .obj or .FBX formats and uploaded to Sketchfab.

Once the model was imported into SF, lighting and background color were adjusted.  The SF generated embed code was copied and pasted onto this page (see Fig. 1).  Click the “Play” button to start the interactivity.

Both the Cryo-EM surface (EMD 2984) and  PDB 5A1A (ribbon formation) were co-exported from 3DS Max and uploaded to Sketchfab.  The surface  opacity was set to 30%, revealing PDB 5A1A underneath the surface (see Fig. 2).

Use the arrows located on the bottom of the viewer ( arows) to navigate to the various positions!

General Information:

Cryo-electron microscopy (3DEM) is a field of structural biology that deals with the determination of 3D structures of macromolecular complexes and cells.   This emerging field helps to bridges the gap between cell biology and crystallography/NMR.

EMDataBank is the unified global portal for the deposition and retrieval of 3DEM density maps, atomic models and associated metadata.

 New advances in electron microscopy reveal molecular structures at resolutions useful for drug discovery.

Produced by Science and the National Cancer Institute.

Animation Credit: Veronica Falconieri and Sriram Subramaniam/LCB/CCR/NCI/NIH

Link to article: http://scim.ag/1dYcNi0

Related studies regarding this structure:

Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy

Alberto Bartesaghi,1 Doreen Matthies,1 Soojay Banerjee, Alan Merk, and Sriram Subramaniam2

The four protomers  of β-galactosidase are indicated on the interactive 3D model above (click on the “annotation” button).  Protomers are usually arranged in cyclical fashion to form closed point group symmetries.  (See: Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy, Fig. 2)