Motif Atlas Releases 1.12 and 1.13
Changes in PDB files used for clustering
Release 1.12 has 218 PDB files, release 1.13 has 220 PDB files, 217 of them are identical.
1 equivalence classes changed representatives: 3SD3 → 4LVZ.
2 new structures in release 1.13: 4JK0, 4NGF.
No equivalence class representatives have been obsoleted.
Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.
Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.
PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.
Redistribution of motif instances
Loading the Sankey diagram...
Changes in motif groups
Release 1.12 has 276 motif groups, release 1.13 has 278 motif groups, 271 of them are identical.
2 motif groups were updated, 3 groups are present only in release 1.12, 5 groups are only in release 1.13.
Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:
Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey
Hover over the links connecting the motif groups to see which motif instances were exchanged.
Identical motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_41766.6 | 54 | Tandem cWW pairs (Not AU or GC) |
| 2 | IL_39199.4 | 53 | Hoogsteen-edge Platform, Single bulged base |
| 3 | IL_56465.4 | 47 | Single, unpaired intercalated base, consensus A |
| 4 | IL_44540.4 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 5 | IL_87904.5 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 6 | IL_82444.1 | 29 | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif |
| 7 | IL_13959.4 | 26 | Double Sheared (tSH-tHS) |
| 8 | IL_65553.8 | 23 | Kink-turn |
| 9 | IL_73276.5 | 22 | C-loop |
| 10 | IL_28947.2 | 22 | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 11 | IL_93424.4 | 21 | tSH-inserted-tHW |
| 12 | IL_55938.4 | 18 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 13 | IL_92027.3 | 17 | 16S h21 S8 binding site |
| 14 | IL_24982.5 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 15 | IL_94430.5 | 16 | 16S h32-h33-h34 3WJ |
| 16 | IL_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 17 | IL_92109.3 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 18 | IL_46648.6 | 13 | 23S H91 IL | Single-Base Intercalation Site |
| 19 | IL_31555.5 | 13 | Tandem sheared with inserted, unpaired purine. |
| 20 | IL_49493.4 | 13 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 21 | IL_43124.2 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 22 | IL_37104.3 | 11 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 23 | IL_17212.2 | 11 | cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif |
| 24 | IL_58291.4 | 10 | Recurrent Sub-motif found in junctions |
| 25 | IL_24546.4 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 26 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 27 | IL_90459.3 | 9 | cWW AG or UU |
| 28 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 29 | IL_02809.3 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 30 | IL_46301.1 | 7 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 31 | IL_25300.3 | 7 | 16S h19 IL and 23S H41 IL |
| 32 | IL_73000.2 | 7 | cHS-cWS |
| 33 | IL_92321.4 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 34 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 35 | IL_90133.3 | 6 | |
| 36 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 37 | IL_70173.1 | 6 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 38 | IL_70237.3 | 6 | |
| 39 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 40 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 41 | IL_97057.3 | 6 | |
| 42 | IL_77263.2 | 6 | Kink-turn from U4 |
| 43 | IL_25380.1 | 6 | LSU Helix 89 (H89) IL2 |
| 44 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 45 | IL_08926.3 | 6 | 23S H91 IL |
| 46 | IL_05684.1 | 5 | tHS tHH bulge with S-turn | Double S-turn motif |
| 47 | IL_79083.3 | 5 | |
| 48 | IL_44067.4 | 5 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 49 | IL_02359.3 | 5 | |
| 50 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 51 | IL_47758.2 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 52 | IL_54966.1 | 4 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 53 | IL_39980.1 | 4 | |
| 54 | IL_48918.3 | 4 | Kink-turn variant |
| 55 | IL_01080.1 | 4 | |
| 56 | IL_98591.3 | 4 | |
| 57 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 58 | IL_82188.2 | 4 | LSU H68 IL from H.m. |
| 59 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 60 | IL_94403.5 | 4 | LSU H77 |
| 61 | IL_42251.1 | 4 | |
| 62 | IL_38807.3 | 4 | |
| 63 | IL_31663.1 | 4 | 23S H73 ILa : Part of larger Motif |
| 64 | IL_09530.1 | 4 | Double S-turn motif |
| 65 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 66 | IL_45262.4 | 4 | |
| 67 | IL_39526.4 | 4 | |
| 68 | IL_28572.2 | 4 | 16S h18 kink-turn like motif |
| 69 | IL_95652.3 | 4 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 70 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 71 | IL_31066.3 | 4 | SSU Helix 44 (h44) extension |
| 72 | IL_97296.1 | 4 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 73 | IL_98421.4 | 3 | SSU Helix 12 (h12) IL |
| 74 | IL_43946.1 | 3 | |
| 75 | IL_06211.3 | 3 | |
| 76 | IL_52173.1 | 3 | |
| 77 | IL_05723.1 | 3 | |
| 78 | IL_58586.2 | 3 | |
| 79 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 80 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 81 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 82 | IL_89028.6 | 3 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th. |
| 83 | IL_28003.1 | 3 | |
| 84 | IL_06180.1 | 3 | tHS tHH bulge with S-turn |
| 85 | IL_16415.2 | 3 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 86 | IL_95150.6 | 3 | |
| 87 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 88 | IL_25271.2 | 3 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 89 | IL_87065.1 | 3 | 23S H91 IL | Single-Base Intercalation Site |
| 90 | IL_30840.2 | 3 | |
| 91 | IL_62499.7 | 3 | |
| 92 | IL_34628.2 | 3 | Kink-turn |
| 93 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 94 | IL_07300.2 | 3 | |
| 95 | IL_80348.3 | 3 | 23S H91 IL |
| 96 | IL_47875.1 | 3 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 97 | IL_35043.1 | 3 | cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base |
| 98 | IL_16166.4 | 3 | 23S H91 IL |
| 99 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 100 | IL_69106.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 101 | IL_97509.1 | 2 | Double sheared with wobble cWW. |
| 102 | IL_45794.1 | 2 | |
| 103 | IL_96446.1 | 2 | |
| 104 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 105 | IL_23262.4 | 2 | |
| 106 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 107 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 108 | IL_16330.1 | 2 | |
| 109 | IL_87507.1 | 2 | tHS tHH bulge with S-turn |
| 110 | IL_50521.1 | 2 | |
| 111 | IL_80093.1 | 2 | |
| 112 | IL_30381.1 | 2 | tHS tHH bulge with S-turn |
| 113 | IL_31039.1 | 2 | |
| 114 | IL_46990.1 | 2 | |
| 115 | IL_43877.1 | 2 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 116 | IL_90735.1 | 2 | |
| 117 | IL_40892.1 | 2 | |
| 118 | IL_33964.1 | 2 | |
| 119 | IL_70401.1 | 2 | |
| 120 | IL_87548.1 | 2 | |
| 121 | IL_24293.1 | 2 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 122 | IL_33842.1 | 2 | |
| 123 | IL_52940.1 | 2 | |
| 124 | IL_09882.1 | 2 | |
| 125 | IL_77076.1 | 2 | |
| 126 | IL_96206.3 | 2 | |
| 127 | IL_46435.1 | 2 | |
| 128 | IL_09587.1 | 2 | |
| 129 | IL_00998.1 | 2 | |
| 130 | IL_23414.1 | 2 | |
| 131 | IL_39355.1 | 2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1 |
| 132 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 133 | IL_11751.1 | 2 | |
| 134 | IL_90057.1 | 2 | |
| 135 | IL_46034.3 | 2 | |
| 136 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 137 | IL_98566.1 | 2 | |
| 138 | IL_12211.1 | 2 | |
| 139 | IL_21495.1 | 2 | |
| 140 | IL_67887.1 | 2 | |
| 141 | IL_21639.1 | 2 | |
| 142 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 143 | IL_97833.1 | 2 | |
| 144 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 145 | IL_37406.1 | 2 | |
| 146 | IL_37197.1 | 2 | |
| 147 | IL_88865.1 | 1 | |
| 148 | IL_25307.1 | 1 | |
| 149 | IL_26868.1 | 1 | |
| 150 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 151 | IL_55649.1 | 1 | |
| 152 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 153 | IL_71942.1 | 1 | |
| 154 | IL_83856.1 | 1 | |
| 155 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 156 | IL_70299.1 | 1 | |
| 157 | IL_57364.1 | 1 | LSU Helix 89 (H89) IL2 |
| 158 | IL_41139.1 | 1 | |
| 159 | IL_23448.1 | 1 | |
| 160 | IL_46721.1 | 1 | |
| 161 | IL_50911.1 | 1 | 16S h34 ILa : Part of larger motif |
| 162 | IL_80714.1 | 1 | |
| 163 | IL_03110.1 | 1 | |
| 164 | IL_02835.1 | 1 | |
| 165 | IL_76263.1 | 1 | |
| 166 | IL_91379.1 | 1 | |
| 167 | IL_11302.1 | 1 | |
| 168 | IL_75328.1 | 1 | |
| 169 | IL_86336.1 | 1 | |
| 170 | IL_81398.1 | 1 | |
| 171 | IL_97842.1 | 1 | |
| 172 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 173 | IL_64589.1 | 1 | |
| 174 | IL_54470.1 | 1 | tHS tHH bulge with S-turn |
| 175 | IL_91044.1 | 1 | |
| 176 | IL_27668.1 | 1 | |
| 177 | IL_41153.1 | 1 | |
| 178 | IL_85805.1 | 1 | |
| 179 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 180 | IL_41791.1 | 1 | |
| 181 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 182 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 183 | IL_89794.1 | 1 | |
| 184 | IL_28644.1 | 1 | |
| 185 | IL_52509.1 | 1 | |
| 186 | IL_27243.1 | 1 | |
| 187 | IL_37347.1 | 1 | |
| 188 | IL_46306.1 | 1 | |
| 189 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 190 | IL_91089.1 | 1 | |
| 191 | IL_06847.1 | 1 | Group II Intron IL |
| 192 | IL_30067.1 | 1 | |
| 193 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 194 | IL_57977.1 | 1 | |
| 195 | IL_39324.1 | 1 | |
| 196 | IL_02897.1 | 1 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th. |
| 197 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 198 | IL_83920.1 | 1 | |
| 199 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 200 | IL_53988.1 | 1 | |
| 201 | IL_31224.1 | 1 | 23S H91 IL |
| 202 | IL_05221.1 | 1 | |
| 203 | IL_06471.1 | 1 | |
| 204 | IL_68767.1 | 1 | |
| 205 | IL_17603.1 | 1 | |
| 206 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 207 | IL_99397.1 | 1 | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 208 | IL_60649.1 | 1 | Kink-turn |
| 209 | IL_52610.1 | 1 | |
| 210 | IL_63952.1 | 1 | |
| 211 | IL_63253.1 | 1 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 212 | IL_11778.1 | 1 | |
| 213 | IL_61730.1 | 1 | |
| 214 | IL_25082.1 | 1 | |
| 215 | IL_53323.1 | 1 | |
| 216 | IL_26971.1 | 1 | |
| 217 | IL_56513.1 | 1 | |
| 218 | IL_15205.1 | 1 | |
| 219 | IL_87523.1 | 1 | |
| 220 | IL_77296.1 | 1 | |
| 221 | IL_87394.1 | 1 | |
| 222 | IL_05513.1 | 1 | |
| 223 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 224 | IL_86059.1 | 1 | |
| 225 | IL_43316.1 | 1 | |
| 226 | IL_12507.1 | 1 | |
| 227 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 228 | IL_06421.1 | 1 | Single sheared with bulged bases |
| 229 | IL_20775.1 | 1 | tSH-inserted |
| 230 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 231 | IL_88119.1 | 1 | |
| 232 | IL_98924.1 | 1 | |
| 233 | IL_59529.1 | 1 | |
| 234 | IL_91904.1 | 1 | |
| 235 | IL_21421.1 | 1 | |
| 236 | IL_85510.1 | 1 | |
| 237 | IL_21077.1 | 1 | |
| 238 | IL_03282.1 | 1 | |
| 239 | IL_42891.1 | 1 | |
| 240 | IL_78513.1 | 1 | |
| 241 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 242 | IL_80505.1 | 1 | |
| 243 | IL_69799.1 | 1 | |
| 244 | IL_47687.1 | 1 | |
| 245 | IL_52958.1 | 1 | |
| 246 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 247 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 248 | IL_25181.1 | 1 | |
| 249 | IL_09491.1 | 1 | |
| 250 | IL_58454.1 | 1 | |
| 251 | IL_88367.1 | 1 | |
| 252 | IL_49527.1 | 1 | |
| 253 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 254 | IL_47732.1 | 1 | |
| 255 | IL_40845.1 | 1 | |
| 256 | IL_06177.1 | 1 | cWW AG or UU |
| 257 | IL_82650.1 | 1 | |
| 258 | IL_22909.1 | 1 | |
| 259 | IL_80652.1 | 1 | |
| 260 | IL_54450.1 | 1 | |
| 261 | IL_77014.1 | 1 | |
| 262 | IL_91078.1 | 1 | |
| 263 | IL_06306.1 | 1 | |
| 264 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 265 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 266 | IL_02957.1 | 1 | |
| 267 | IL_18675.1 | 1 | cWW-bulge-cWW |
| 268 | IL_40527.1 | 1 | Kink-turn |
| 269 | IL_49976.1 | 1 | |
| 270 | IL_57285.1 | 1 | |
| 271 | IL_13777.1 | 1 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_97217.11 | 248 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_47174.11 | 219 | cWW AG or water inserted cWW Y-Y. |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_21644.1 | 2 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 2 | IL_12024.1 | 2 | |
| 3 | IL_03741.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_12147.1 | 2 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 2 | IL_27640.1 | 1 | |
| 3 | IL_37325.1 | 1 | |
| 4 | IL_63133.1 | 1 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 5 | IL_17066.1 | 1 |