Center for the Molecular Biology of RNA

3.0 Å RF2 bound 70S Termination Complex

70S_RF2.pdb.tgz (13 MB)
(updated 12/8/2008)

The PDB file contains the two 70S ribosome copies in the crystallographic asymmetric unit. Each copy includes the 30S and 50S subunits, messenger RNA, P- and E-site tRNA and release factor 2 bound in the A site in response to a UAA stop codon on the mRNA.

The MTZ file contains the structure factor amplitudes against which the model was refined.

When using these files, please reference:
A. Korostelev, H. Asahara, L. Lancaster, M. Laurberg, A. Hirschi, J. Zhu, S. Trakhanov, W.G. Scott and H.F. Noller
Crystal structure of a translation termination complex formed with release factor RF2.
Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19684-9.
(Epub 2008 Dec 8)

Protein Data Bank links : 3F1E | 3F1F | 3F1G | 3F1H

3.2 Å RF1 bound 70S Termination Complex

70S_RF1.pdb.tgz (13 MB)
(updated 8/20/2008)

The PDB file contains the two 70S ribosome copies in the crystallographic asymmetric unit. Each copy includes the 30S and 50S subunits, messenger RNA, P- and E-site tRNA and release factor 1 bound in the A site in response to a UAA stop codon on the mRNA.

The MTZ file contains the structure factor amplitudes against which the model was refined.

This PYMOL script provides easy means of inspecting the structure.

When using these files, please reference:
M. Laurberg, H. Asahara, A. Korostelev, S. Trakhanov and H.F. Noller (2008)
Structural basis for translation termination on the 70S ribosome.
Nature 454, 852-857 (14 August 2008)

abstract | full text | pdf | supplementary information | more images | CNS Stack add-on |

Protein Data Bank links : 3D5A | 3D5B | 3D5C | 3D5D

3.7 Å 70S Ribosome PDB

70S_ribosome3.7A_model140.pdb.gz (2.3 MB)
(updated 4/23/2007)

This PDB file contains the entire 70S ribosome, including the 30S subunit (16S rRNA and small subunit proteins), 50S subunit (23S rRNA, 5S rRNA, and large subunit proteins), P- and E-site tRNA, and messenger RNA.

When using this file, please reference:
A. Korostelev, S. Trakhanov, M. Laurberg and H.F. Noller (2006) Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements. Cell 126:1065–1077.
summary | full text | pdf

5.5 Å 70S Ribosome PDB files

pdb1gix.ent (880 KB)

This PDB file contains the 30S subunit including 16S rRNA, small subunit proteins, A-, P- and E-site tRNA, and messenger RNA. A summary of the chain IDs and sequence are available at the RCSB.

pdb1giy.ent (555 KB)

This PDB file contains the 50S subunit including 23S rRNA and large subunit proteins as well as the 5S rRNA. A summary of the chain IDs and sequence are available at the RCSB.

PDB files and macros for viewing the Ribosome in 'O'

ribosome.tar.gz (1.25 MB)

A package of 70S ribosome PDB coordinate files, macros and instructions necessary to build a complete complex in O.

70S.odb.gz (800 KB)

A 70S database prebuilt for O version 8.0.6.

See the 'O' Home Page at the Uppsala Software Factory for more information about the program O.

PDB files and macros for viewing the Ribosome in 'RasMol'

rasmol.tar.gz (260 KB)

A package containing a 70S PDB file suitable for RasMol, and scripts for coloring and labeling. The model can be displayed using the "backbone" display command or menu option in Rasmol.

See the Rasmol Home Page maintained by Dr. Eric Martz at the University of Massachusetts Amherst for more information about RasMol, RasMac, and RasWin.