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. After download, you can verify file integrity by comparing md5sum, sha256 or sha512 values. Go to: Data Sets    File Name Convention    File Descriptions    Updates/Corrections

Current data sets (last updated Nov 13, 2024)

LSU-SSU assemblies (1522 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 (413 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 (572 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 (63 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:

Angle 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

• RCSB - RCSB entry associated with the structure
• RCSB version - The version of the structure that was used for RAD calculations
• notes - This is rarely populated. It contains information pertaining to RAD angle calculation protocols for specific structures. For example, it is sometimes only possible to align the SSU and not the LSU. In that case, the structure would appear in the "Isolated SSUs" data set, even though the model contains a LSU. This column also may contain information about values that have been changed in the RCSB database (e.g. reported resolution values). For those structures, it will be noted in this column. Organism names also sometimes change in RCSB, though these changes are not recorded in the RAD database.
• LSU chain - "Original chain ID" of the large subunit rRNA (defined in the RCSB mapping file associated with a PDB bundle)
• SSU chain - "Original chain ID" of the small subunit rRNA
• method - experimental method used (EM/XRAY). value obtained from RCSB
• resolution - experimental resolution (in Å). value for resolution_combined extracted from RCSB.
• organism - organism associated with the longest rRNA chain. If the two longest chains are of the same length and have different organism entries (e.g. E. coli vs. E. coli K-12), one is randomly selected. value obtained from RCSB
• domain - domain of life for organism. This value is manually assigned. Let us know if you believe you found an error.
• mito - Is this a mitoribosome, yes, or no? If "mitoribo" or "mitochond" match the RCSB title value (case-insensitive), or if any polymer name matches "mito", then this is given the value "yes".

Rotation angles and displacements

The following quantities were calculated using RADtool with default settings.

• body rot. - rotation angle of the SSU body (relative to the reference classical E. coli structure)
• body tilt - tilt angle of the SSU body
• body tilt dir. - tilt direction of the SSU body
• body trans. - translational displacement of the SSU body (i.e. any displacement that can not be described by a rotation)
• head rot. - rotation angle of the SSU head
• head tilt - tilt angle of the SSU head
• head tilt dir. - tilt direction of the SSU head
• head trans. - translational displacement of the SSU head

Structure alignment information

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

• LSU core res. - number of residues in the LSU rRNA that align to within 2 Å with the reference E. coli structure.
• body core res. - number of residues in the SSU rRNA body that align to within 2 Å with the reference E. coli structure
• head core res. - number of residues in the SSU rRNA head that align to within 2 Å with the reference E. coli structure
• LSU RMSD - RMSD of the LSU core residues, with respect to the reference E. coli structure
• body RMSD - RMSD of the SSU body core residues
• head RMSD - RMSD of the SSU head core residues

Publication Information

These values are obtained directly from RCSB.

• authors - author list
• year - year of publication
• journal - journal
• volume - volume
• page/article - first page number, or article number

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.

• < rscc > LSU core - average rscc value for core residues in the LSU
• < rsr > LSU core - average rsr value for core residues in the LSU
• < rsrz > LSU core - average rsrz value for core residues in the LSU
• < Q_score > LSU core - average Q-score value for core residues in the LSU
• < residue_inclusion > LSU core - average residue inclusion value for core residues in the LSU
• < rscc > BODY core - average rscc value for core residues in the SSU body
• < rsr > BODY core - average rsr value for core residues in the SSU body
• < rsrz > BODY core - average rsrz value for core residues in the SSU body
• < Q_score > BODY core - average Q-score value for core residues in the SSU body
• < residue_inclusion > BODY core - average residue inclusion value for core residues in the SSU body
• < rscc > HEAD core - average rscc value for core residues in the SSU head
• < rsr > HEAD core - average rsr value for core residues in the SSU head
• < rsrz > HEAD core - average rsrz value for core residues in the SSU head
• < Q_score > HEAD core - average Q-score value for core residues in the SSU head
• < residue_inclusion > HEAD core - average residue inclusion value for core residues in the SSU head

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.

November 3, 2023: In order to enable tracking of RCSB versioning, all values in the database were regenerated using the most recent revisions of all RCSB entries. Since a newer CPU was used (Mac M2), and some RCSB entries had been updated, there were minor differences in some quantities (0.1 degrees, or 0.001 Angstroms). A complete list of associated changes can be found here.

March 1, 2023: Back-end scripts that calculate translational displacements were updated. As a result, rounding differences introduced a few changes to the values of some translations (less than 0.01 Angstrom).

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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