Volume of 70S (intact) ribosome including salt ions and spermidine

Value 3400 nm^3
Organism Bacteria Escherichia coli
Reference Zhu J, Penczek PA, Schröder R, Frank J. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. J Struct Biol. 1997 Apr118(3):197-219 p.213 left column bottom paragraph & right column top paragraphPubMed ID9169230
Method (Ref abstract:) "Cryoelectron microscopy provides the means of studying macromolecules in their native state. However, the contrast transfer function (CTF) makes the images and the three-dimensional (3D) maps derived from them difficult to interpret. Resarchers developed methods to determine the CTF from experimental data and to obtain a CTF-corrected 3D reconstruction. The CTF correction and 3D reconstruction accomplished in one step made it easy to combine different defocus data sets and decrease the error accumulation in the computation."
Comments "The surface representation of the merged reconstruction from three data sets at the density corresponding to a volume size of 2.4×10^6 Å3 is shown in Fig. 9b. The surface of the ribosome is seen to be very fragmented (see Stark et al., 1995, where this choice of volume was used). However, the calculation of chemical molecular weight does not include the presence of salt ions, e.g., Mg2+ and K+, and of spermidine in the ribosome. The ribosome volume estimates from air-dried EM [electron microscopy] are between 3.00 and 3.56×10^6 Å^3 the estimate from freezedried EM is even as high as 5.1×10^6 Å^3 (van Holde and Hill, 1974). Considering all these factors, [researchers] assume a volume increase by 40% from the value derived from the chemical mass (BNID 100122), to a total of 3.4×10^6 Å^3. Therefore, the density threshold giving a volume of 3.4×10^6 Å^3 was used for all surface representations except the one presented in Fig. 9b." See BNID 102475 (Solvent-excluded Volume of 50S ribosome)
Entered by Uri M
ID 104919