Download Current Database

We regularly update the database in order to provide current information on every ribosome structure that has been published. The data sets may be accessed and queried through our webtools, or they may be downloaded. The data is provided in CSV format, so that they can easily be imported using Excel, or other spreadsheet software.
Go to: Data Sets    File Name Convention    File Descriptions    Updates/Corrections

Current data sets (last updated Nov 23, 2022)

LSU-SSU assemblies (1209 entries) - This data set includes structures that contain an LSU and SSU. This list only includes structures for which RADtool was able to separately perform STAMP alignment of the LSU, SSU body and SSU head to an E. coli structure. The data file contains information about the alignment process, calculated rotation/tilt angles of the head and body, as well as organism and experimental information. Note: When compiling this list, we only include structures for which the LSU and SSU are associated with the same RCSB accession code. If STAMP structure alignment for an LSU-SSU assembly failed for either subunit (e.g. LSU of Trypanosoma brucei), then the model will be listed in one of the data sets below. LSU-SSU validation statistics

Isolated SSUs (334 entries) - This data set includes structures that only contain an SSU (e.g. initiation complex and assembly intermediates). This list includes structures for which STAMP alignment was able to successfully align the body and head domain to E. coli. The file contains information about the alignment steps, as well as the rotation/tilt angles of the SSU head domain. SSU-only validation statistics

Isolated LSUs (386 entries) - This data set includes structures that only contain an LSU. The list includes structures for which STAMP alignment was successfully applied. LSU-only validation statistics

Structures not included in the above data sets (35 entries) - In some cases, it is not possible to align the LSU and/or the SSU body and/or head domains to E. coli. For completeness, we also include this list of structures for which alignment was not successful (e.g. partially folded intermediates, atypical structures, fragments of subunits).

Data set file naming convention

The database files are named with the following conventions:

Angular decomposition files

File name: RADdb.< date >.< assembly >.csv
< date > is the date last updated (YYYYMMDD format).
< assembly > can be "LSUSSU", "SSU" (isolated SSUs) or "LSU" (isolated LSUs).

Validation statistics files

File name: RADdb.< date >.< assembly >.validationstats.csv
< date > is the date last updated (YYYYMMDD format).
< assembly > can be "LSUSSU", "SSU" (isolated SSUs) or "LSU" (isolated LSUs).

Description of data files

Each data set listed above is provided in CSV format. Below is a description of the information provided in each column.

Structure and organism data

Rotation angles and displacements

The following quantities were calculated using RADtool with default settings.

Structure alignment information

These quantities were calculated using RADtool with default structure-alignment settings applied.

Publication Information

These values are obtained directly from RCSB.

Validation Statistics

These quantities are calculated from per-residue values provided by RCSB model validation reports. All quantities represent averages over the core residues of each subunit/domain.

Format Updates and Corrections

While we will try to minimize the number of format changes, we may sometimes need to adjust the database file formats (e.g. correct an error, add new information). If any changes to the database file formats are introduced, they will be listed here.

October 24, 2022: Some entries were listed with their mmCIF chain IDs, rather than the Original Chain IDs. The issue has been resolved.

August 22, 2022: Two entries were found to be listed more than once (with identical values). Also, some recently-published structures (June-August 2022) were listed with the chain IDs that are given in the PDB files, rather than the "Original" IDs. Both issues have been resolved.

July 21, 2022: Some systems listed in the "Structures not included in the above data sets" list were inadvertently also listed in the Isolate SSU data set. These had artificially large rotation/tilt values, and they have since been removed.

July 20, 2022 : For entries that had missing publication elements (e.g. year, journal, etc), the publication values were sometimes shifted by one column. Most notably, page numbers sometimes would appear under the volume column. This has been corrected.

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