Release idAll changesDateNumber of IFEs
3.359 (current)11 changes2024-10-3018329
3.35817 changes2024-10-2318314
3.35724 changes2024-10-1618277
3.35614 changes2024-10-0918235
3.35519 changes2024-10-0218205
3.35421 changes2024-09-2518168
3.35314 changes2024-09-1818142
3.35231 changes2024-09-1118099
3.35120 changes2024-09-0418047
3.35010 changes2024-08-2818021
3.34916 changes2024-08-2117999
3.34817 changes2024-08-1417964
3.34722 changes2024-08-0717921
3.34625 changes2024-07-3117803
3.34542 changes2024-07-2517763
3.34442 changes2024-07-1717684
3.34332 changes2024-07-1017638
3.3428 changes2024-07-0317571
3.34117 changes2024-06-2617545
3.34012 changes2024-06-1917512
3.339249 changes2024-06-1217474
3.33816 changes2024-06-0517274
3.33714 changes2024-05-2917222
3.33620 changes2024-05-2217146
3.33525 changes2024-05-1517078
3.33410 changes2024-05-0817047
3.333438 changes2024-05-0117037
3.33213 changes2024-04-2416940
3.33112 changes2024-04-1716921
3.33010 changes2024-04-1016903
3.3298 changes2024-04-0316887
3.32814 changes2024-03-2716871
3.32723 changes2024-03-2016841
3.32618 changes2024-03-1316805
3.32538 changes2024-03-0616787
3.32416 changes2024-02-2816678
3.32329 changes2024-02-2116626
3.32210 changes2024-02-1416539
3.32121 changes2024-02-0716521
3.32018 changes2024-01-3116486
3.31938 changes2024-01-2416466
3.31827 changes2024-01-1716336
3.31727 changes2024-01-1016306
3.3161 changes2024-01-0316270
3.31534 changes2023-12-2716269
3.31430 changes2023-12-2016151
3.31310 changes2023-12-1316115
3.31248 changes2023-12-0616100
3.31130 changes2023-11-2916002
3.31012 changes2023-11-2415969
3.30914 changes2023-11-1515949
3.3088 changes2023-11-0815923
3.30712 changes2023-11-0115911
3.30613 changes2023-10-2515898
3.3059 changes2023-10-1815861
3.30410 changes2023-10-1115844
3.3037 changes2023-10-0415833
3.30210 changes2023-09-2715825
3.30115 changes2023-09-2015806
3.3004 changes2023-09-1315741
3.29926 changes2023-09-0615737
3.29817 changes2023-08-3015699
3.2978 changes2023-08-2315677
3.29628 changes2023-08-1615656
3.29518 changes2023-08-0915571
3.2949 changes2023-08-0215504
3.29310 changes2023-07-2615489
3.29227 changes2023-07-1915445
3.29114 changes2023-07-1215401
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3.28517 changes2023-05-3115192
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3.28321 changes2023-05-1715152
3.2827 changes2023-05-1015121
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3.2806 changes2023-04-2615095
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3.27116 changes2023-02-2214742
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3.26615 changes2023-01-1814622
3.26514 changes2023-01-1114594
3.2643 changes2023-01-0414580
3.26319 changes2022-12-2814574
3.2629 changes2022-12-2114548
3.26111 changes2022-12-1414523
3.26014 changes2022-12-0714501
3.25924 changes2022-11-3014487
3.25811 changes2022-11-2314429
3.25735 changes2022-11-1614332
3.25617 changes2022-11-0914277
3.25512 changes2022-11-0214249
3.25422 changes2022-10-2614231
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3.2499 changes2022-09-2114071
3.2488 changes2022-09-1414055
3.24720 changes2022-09-0714041
3.24610 changes2022-08-3114013
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3.2445 changes2022-08-1713983
3.24311 changes2022-08-1013978
3.24226 changes2022-08-0313952
3.2415 changes2022-07-2713918
3.24014 changes2022-07-2013904
3.23927 changes2022-07-1313887
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3.23115 changes2022-05-1813484
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3.2296 changes2022-05-0413437
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3.22320 changes2022-03-2313332
3.22228 changes2022-03-1613289
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3.2122 changes2022-01-0512920
3.2116 changes2021-12-2912914
3.2102 changes2021-12-2212907
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3.20718 changes2021-12-0112676
3.2065 changes2021-11-2412633
3.20522 changes2021-11-1712615
3.2046 changes2021-11-1012576
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3.20212 changes2021-10-2712540
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3.1981 changes2021-09-2912433
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3.1935 changes2021-08-2512264
3.19216 changes2021-08-1812259
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3.19011 changes2021-08-0412215
3.18922 changes2021-07-2812219
3.18812 changes2021-07-2112151
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3.1859 changes2021-06-3012046
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3.18211 changes2021-06-0911989
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3.17610 changes2021-04-2811790
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3.1713 changes2021-03-2411733
3.17016 changes2021-03-1711728
3.1699 changes2021-03-1011716
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3.1604 changes2021-01-0611648
3.15916 changes2020-12-3011644
3.15828 changes2020-12-2311623
3.1574 changes2020-12-1611530
3.15617 changes2020-12-0911523
3.1559 changes2020-12-0211503
3.15410 changes2020-11-2511490
3.1534 changes2020-11-1811462
3.15236 changes2020-11-1111457
3.151110 changes2020-11-0411388
3.1509 changes2020-10-2811509
3.1497 changes2020-10-2111494
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3.1435 changes2020-09-0911189
3.14224 changes2020-09-0211182
3.14122 changes2020-08-2610963
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3.1395 changes2020-08-1210875
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3.13724 changes2020-07-2910839
3.13612 changes2020-07-2210781
3.1357 changes2020-07-1510734
3.13418 changes2020-07-0810724
3.13310 changes2020-07-0110641
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3.1247 changes2020-04-2910374
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3.1201 changes2020-04-0110312
3.1190 changes2020-03-2510311
3.1185 changes2020-03-1810311
3.11718 changes2020-03-1110305
3.1169 changes2020-03-0410285
3.1154 changes2020-02-2610266
3.11413 changes2020-02-1910261
3.1133 changes2020-02-1210246
3.1127 changes2020-02-0510244
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3.1102 changes2020-01-2210219
3.10912 changes2020-01-1510217
3.1082 changes2020-01-0810208
3.10720 changes2020-01-0110204
3.10621 changes2019-12-2510172
3.1050 changes2019-12-1810117
3.1044 changes2019-12-1110117
3.10311 changes2019-12-0410113
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3.9885 changes2019-10-3010013
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3.963 changes2019-10-169999
3.954 changes2019-10-099990
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3.911 changes2019-09-119894
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3.834 changes2019-07-199725
3.820 changes2019-07-129719
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3.8014 changes2019-06-289681
3.7923 changes2019-06-219646
3.7819 changes2019-06-149555
3.778 changes2019-06-079518
3.7613 changes2019-05-319505
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3.732 changes2019-05-109463
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3.7113 changes2019-04-269459
3.7026 changes2019-04-199437
3.6910 changes2019-04-129382
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3.673 changes2019-03-299348
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3.583 changes2019-01-259160
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3.563 changes2019-01-119131
3.551 changes2019-01-049126
3.543 changes2018-12-289125
3.5310 changes2018-12-219123
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1.102013-05-112489
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1.62013-04-132457
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1.42013-03-302439
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1.04 changes2013-03-022427
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0.1062013-01-262387
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0.1042013-01-122369
0.1032013-01-052367
0.1022012-12-292367
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0.1599 changes2011-02-051630

We moved to a new server on September 10, 2024. Release 3.352 looks good. Basepair annotations for new structures are now being done by fr3d-python and not the older Matlab code.

The Representative Sets of RNA 3D Structures organize all RNA-containing 3D structures from PDB into sequence/structure equivalence classes and selects a high-quality representative structure from each class. The resulting Representative Sets of RNA 3D structures are appropriate for tasks which require searching or training over the breadth of the entire RNA 3D structure database, but which should avoid the redundancy inherent in PDB due to multiple 3D structures of the same molecule from the same organism. Equivalence classes show all structures of the same molecule, and the associated heat maps show all-against-all geometric comparisons of the structures within each class.

Releases are generated weekly, and previous releases are available starting from 2011. The default listing shows structures at 4 Angstrom resolution or better, but different resolution thresholds are available for each release. The set of representative structures can be viewed online along with information about the resolution, experimental method, molecule name, species, and number of equivalent structures. Releases can also be downloaded and parsed by computer programs. Some weeks, when many new structures are released, the representative set listing can be delayed because of the time it takes to compute all-against-all geometric comparisons within large equivalences classes such as Thermus thermophilus small ribosomal subunit.

With release 3.339, we fixed problems with some files that could not be processed, such as 3ZP8, and produced IFEs between "structured" and "unstructured" chains including, for example, 3ZP8|1|A and 3ZP8|1|B, for the first time. That resulted in a number of new or changed equivalence classes.

With release 3.333, we improved the treatment of taxonimic ids, mapping the taxid associated with the PDB chain to a single taxid for the species, so that different strains of the same organism will be grouped together into a single equivalence class. This resulted in unusually many changes to equivalence classes.

With release 3.0, we modified the procedure for choosing the representative of each equivalence class. The representative is now chosen as the IFE (Integrated Functional Element) which optimizes a combination of resolution, RSR, RSCC, Rfree, percent of nucleotides with steric clashes, and the fraction of the molecule observed. The intention is to select the structure with the best experimental evidence for the coordinates being reported. Details will be provided in an upcoming publication.

Individual chains are named in the format XXXX|M|C, where XXXX is the PDB entry, M is the model number, usually 1, and C is the chain identifier, one to four characters. IFEs are made up of individual chains linked with + signs.

With release 2.0, we upgraded the BGSU RNA 3D Hub Site to include new RNA 3D structures distributed in mmCIF format. Some RNA-containing mmCIF structures are very large, containing multiple full ribosomes. Most of the individual RNA molecules of interest occur as single covalently-bonded chains (e.g., tRNA, small ribosomal subunit) but others occur as two or more chains that are strongly coupled by persistent RNA basepairing (e.g., eukaryotic large ribosomal subunit with 5.8S RNA). We refer to these single or coupled chains as Integrated Functional Elements (IFEs). We extract IFEs from each 3D structure file, compare them to one another by sequence and geometry, and group together those which share highly similar sequence, geometry, and species, if known. The groups are referred to as sequence/structure Equivalence Classes. Before release 3.0, the representative of each equivalence class was chosen as the structure with the most annotated basepairs per nucleotide, as a proxy for modeling quality.

Note that the representative sets were formerly referred to as non-redundant lists, but in fact these lists have one instance of homologous IFEs from each species, so they have some redundancy at the level of molecule.

Unique and stable ids are assigned to all equivalence classes of structure files. Representative sets are updated automatically every week, and a versioning system is implemented to provide independent access to data snapshots.

Notice PDB files with no full nucleotides are not included in the representative sets. For example, see PDB 1DV4.


Please use the following citation when using this resource:

Leontis, N. B., & Zirbel, C. L. (2012). Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking. In RNA 3D Structure Analysis and Prediction N. Leontis & E. Westhof (Eds.), (Vol. 27, pp. 281–298). Springer Berlin Heidelberg. doi:10.1007/978-3-642-25740-7_13

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