Structure model of 16S rRNA decoding region 


A model of the decoding region from the Escherichia coli 16S rRNA from the small ribosomal subunit was constructed in a step-wise fashion. Helices 28, 44a, 44b and the central pseudoknot (helices 1 and 2) from the secondary structure were modeled individually using the MC-SYM modeling package. Experimental data including base-pairings and base-triples determined from comparative sequence studies, information from chemical probing experiments, crosslinking data, and nucleotide geometry information using the ISOPAIR program was used to construct the models. Each model was energy optimized and arranged in space to meet tertiary constraints such as tRNA position inoformation and s4U crosslinking data.
 

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MC-SYM files
Saving the file with a .m extension allows the script to be run as is using MC-SYM.
Saving the file with a .doc extension will allow the script to be read as a text file.

PDB files
These .pdb files may be viewed with Rasmol or other graphics program.
 



 
helix44a.m
.pdb file to be used with script: .pdb
helix44a.pdb
helix44b.m
helix44b.pdb
centralpseudoknot.m
centralpseudoknot.pdb
helix28.m
helix28.pdb
decoding.pdb