3J3W

Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a)

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J01
experimental model	PDB	2AW4

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	27652
Reported Resolution (Å)	10.7
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 coefficient
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.

Data Acquisition
Detector Type	FEI EAGLE (4k x 4k)
Electron Dose (electrons/Å**2)	20

Imaging Experiment	1
Date of Experiment	2011-12-06
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	4000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	59000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
MODEL FITTING	MDFF
MODEL FITTING	MODELLER
MODEL FITTING	modeRNA
MODEL FITTING	S2S
RECONSTRUCTION	RELION

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
	Each particle

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.