Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)
ELECTRON MICROSCOPY
Sample
Immature 50S subunit from YlqF-deficient Bacillus subtilis strain
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
21020
Reported Resolution (Å)
13.3
Resolution Method
OTHER
Other Details
(Single particle details: This is one of the classified groups with the software RELION) (Single particle--Applied symmetry: C1)
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (2J01)
2 (2AW4)
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Cross-correlation
Overall B Value
Fitting Procedure
Details
METHOD--Flexible fitting REFINEMENT PROTOCOL--Atom models of the 23S and 5S
rRNAs were built using the software S2S and modeRNA, with the crystal
st ...
METHOD--Flexible fitting REFINEMENT PROTOCOL--Atom models of the 23S and 5S
rRNAs were built using the software S2S and modeRNA, with the crystal
structures of the 50S subunits from E. coli (PDB ID- 2AW4) and Thermus
thermophilus (PDB ID- 2J01) as template. Models of ribosomal proteins, L1, L3,
L4, L6, L10, L13, L14, L15, L17, L19, L20, L21, L22, L23, L24, L27, L29, L30,
L31, L32, L33, L34, L35 and L36 were downloaded from the SWISS-MODEL
Repository. The others, including L2, L5, L11, L16, L18 and L28 were modeled
using MODELLER with crystal structures of E. coli and T. thermophilus 50S
subunits as templates.The combined atomic model of the B. subtilis 50S subunit
was docked into a high resolution mature 50S density map and optimized using
MDFF. This optimized model was docked into the EM density using Chimera and
flexible fitted into the density using MDFF. DETAILS--Ref- Schuwirth, B.S.,
Borovinskaya, M.A., Hau, C.W., Zhang, W., Vila-Sanjurjo, A., Holton, J.M. and
Cate, J.H. (2005) Structures of the bacterial ribosome at 3.5 A resolution.
Science, 310, 827-834. Selmer, M., Dunham, C.M., Murphy, F.V.t., Weixlbaumer,
A., Petry, S., Kelley, A.C., Weir, J.R. and Ramakrishnan, V. (2006) Structure
of the 70S ribosome complexed with mRNA and tRNA. Science, 313, 1935-1942.
Jossinet, F. and Westhof, E. (2005) Sequence to Structure (S2S)- display,
manipulate and interconnect RNA data from sequence to structure.
Bioinformatics, 21, 3320-3321. Rother, M., Rother, K., Puton, T. and Bujnicki,
J.M. (2011) ModeRNA- a tool for comparative modeling of RNA 3D structure.
Nucleic acids research, 39, 4007-4022. Kiefer, F., Arnold, K., Kunzli, M.,
Bordoli, L. and Schwede, T. (2009) The SWISS-MODEL Repository and associated
resources. Nucleic acids research, 37, D387-392. Eswar, N., Webb, B.,
Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.Y., Pieper, U. and
Sali, A. (2006) Comparative protein structure modeling using Modeller. Current
protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et
al.], Chapter 5, Unit 5 6. Trabuco, L.G., Villa, E., Mitra, K., Frank, J. and
Schulten, K. (2008) Flexible fitting of atomic structures into electron
microscopy maps using molecular dynamics. Structure, 16, 673-683. Pettersen,
E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. and
Ferrin, T.E. (2004) UCSF Chimera--a visualization system for exploratory
research and analysis. Journal of computational chemistry, 25, 1605-1612.
