Motif Atlas Releases 1.3 and 1.4
Changes in PDB files used for clustering
Release 1.3 has 200 PDB files, release 1.4 has 201 PDB files, 200 of them are identical.
No equivalence class representatives have been replaced.
1 new structures in release 1.4: 4KYY.
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
Changes in motif groups
Release 1.3 has 271 motif groups, release 1.4 has 271 motif groups, 269 of them are identical.
2 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.
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_97217.6 | 239 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_39199.3 | 54 | Hoogsteen-edge Platform, Single bulged base |
| 3 | IL_41766.3 | 49 | Tandem cWW pairs (Not AU or GC) |
| 4 | IL_56465.3 | 46 | Single, unpaired intercalated base, consensus A |
| 5 | IL_44540.3 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 6 | IL_87904.4 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 7 | IL_06390.3 | 26 | cWH basepair with syn base |
| 8 | IL_13959.3 | 24 | Double Sheared (tSH-tHS) |
| 9 | IL_93424.3 | 22 | tSH-inserted-tHW |
| 10 | IL_65553.5 | 22 | Kink-turn |
| 11 | IL_73276.3 | 21 | C-loop |
| 12 | IL_28947.1 | 21 | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 13 | IL_55938.3 | 18 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 14 | IL_92027.3 | 17 | 16S h21 S8 binding site |
| 15 | IL_24982.4 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 16 | IL_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 17 | IL_92109.1 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 18 | IL_94430.4 | 15 | 16S h32-h33-h34 3WJ |
| 19 | IL_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 20 | IL_49493.3 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 21 | IL_43124.1 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 22 | IL_46648.2 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 23 | IL_21304.2 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 24 | IL_24546.3 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 25 | IL_58291.3 | 9 | Recurrent Sub-motif found in junctions |
| 26 | IL_02809.2 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 27 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 28 | IL_90459.3 | 9 | cWW AG or UU |
| 29 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 30 | IL_73000.2 | 7 | cHS-cWS |
| 31 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 32 | IL_92321.3 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 33 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 34 | IL_70237.3 | 6 | |
| 35 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 36 | IL_97057.3 | 6 | |
| 37 | IL_90133.2 | 6 | |
| 38 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 39 | IL_44067.3 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 40 | IL_54420.1 | 6 | |
| 41 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 42 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 43 | IL_77263.1 | 5 | Kink-turn from U4 |
| 44 | IL_92484.1 | 5 | |
| 45 | IL_02359.3 | 5 | |
| 46 | IL_78732.3 | 5 | Double S-turn motif |
| 47 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 48 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 49 | IL_16207.1 | 5 | Single sheared with bulged bases |
| 50 | IL_79083.3 | 5 | |
| 51 | IL_08926.2 | 5 | 23S H91 IL |
| 52 | IL_25300.1 | 5 | 16S h19 IL and 23S H41 IL |
| 53 | IL_45262.3 | 5 | |
| 54 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 55 | IL_01080.1 | 4 | |
| 56 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 57 | IL_42251.1 | 4 | |
| 58 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 59 | IL_98591.3 | 4 | |
| 60 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 61 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 62 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 63 | IL_94403.1 | 4 | LSU H77 |
| 64 | IL_16166.3 | 4 | 23S H91 IL |
| 65 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 66 | IL_38807.3 | 4 | |
| 67 | IL_08559.1 | 4 | LSU Helix 89 (H89) IL2 |
| 68 | IL_39526.4 | 4 | |
| 69 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 70 | IL_48918.2 | 3 | Kink-turn variant |
| 71 | IL_62499.6 | 3 | |
| 72 | IL_80348.1 | 3 | 23S H91 IL |
| 73 | IL_89028.5 | 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. |
| 74 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 75 | IL_98421.3 | 3 | SSU Helix 12 (h12) IL |
| 76 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 77 | IL_09520.2 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 78 | IL_30840.1 | 3 | |
| 79 | IL_34156.6 | 3 | cWW AG or UU |
| 80 | IL_58586.2 | 3 | |
| 81 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 82 | IL_43946.1 | 3 | |
| 83 | IL_56077.1 | 3 | |
| 84 | IL_34628.2 | 3 | Kink-turn |
| 85 | IL_52173.1 | 3 | |
| 86 | IL_71565.3 | 3 | |
| 87 | IL_75447.1 | 3 | |
| 88 | IL_05723.1 | 3 | |
| 89 | IL_92267.1 | 3 | 23S H73 ILa : Part of larger Motif |
| 90 | IL_10647.1 | 3 | tHS tHH bulge with S-turn |
| 91 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 92 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 93 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 94 | IL_95150.3 | 3 | |
| 95 | IL_09348.5 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 96 | IL_11751.1 | 2 | |
| 97 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 98 | IL_33925.1 | 2 | |
| 99 | IL_55287.1 | 2 | |
| 100 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 101 | IL_91273.1 | 2 | |
| 102 | IL_33964.1 | 2 | |
| 103 | IL_37406.1 | 2 | |
| 104 | IL_46435.1 | 2 | |
| 105 | IL_98566.1 | 2 | |
| 106 | IL_12211.1 | 2 | |
| 107 | IL_21495.1 | 2 | |
| 108 | IL_27892.1 | 2 | |
| 109 | IL_49550.1 | 2 | tHS tHH bulge with S-turn |
| 110 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 111 | IL_90057.1 | 2 | |
| 112 | IL_09587.1 | 2 | |
| 113 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 114 | IL_19898.1 | 2 | |
| 115 | IL_40892.1 | 2 | |
| 116 | IL_50521.1 | 2 | |
| 117 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 118 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 119 | IL_07300.1 | 2 | |
| 120 | IL_09882.1 | 2 | |
| 121 | IL_23262.4 | 2 | |
| 122 | IL_87548.1 | 2 | |
| 123 | IL_09901.1 | 2 | tHS tHH bulge with S-turn |
| 124 | IL_23414.1 | 2 | |
| 125 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 126 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 127 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 128 | IL_00998.1 | 2 | |
| 129 | IL_16252.3 | 2 | 23S H91 IL |
| 130 | IL_28942.1 | 2 | |
| 131 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 132 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 133 | IL_88180.1 | 2 | cWW-bulge-cWW |
| 134 | IL_97833.1 | 2 | |
| 135 | IL_01054.1 | 2 | |
| 136 | IL_16330.1 | 2 | |
| 137 | IL_24358.1 | 2 | |
| 138 | IL_37197.1 | 2 | |
| 139 | IL_45794.1 | 2 | |
| 140 | IL_52940.1 | 2 | |
| 141 | IL_77076.1 | 2 | |
| 142 | IL_80093.1 | 2 | |
| 143 | IL_03741.1 | 1 | |
| 144 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 145 | IL_26868.1 | 1 | |
| 146 | IL_30067.1 | 1 | |
| 147 | IL_37347.1 | 1 | |
| 148 | IL_46306.1 | 1 | |
| 149 | IL_52958.1 | 1 | |
| 150 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 151 | IL_85805.1 | 1 | |
| 152 | IL_03931.1 | 1 | 16S h19 IL and 23S H41 IL |
| 153 | IL_06471.1 | 1 | |
| 154 | IL_09491.1 | 1 | |
| 155 | IL_11778.1 | 1 | |
| 156 | IL_15205.1 | 1 | |
| 157 | IL_17603.1 | 1 | |
| 158 | IL_21421.1 | 1 | |
| 159 | IL_26971.1 | 1 | |
| 160 | IL_30354.1 | 1 | |
| 161 | IL_40527.1 | 1 | Kink-turn |
| 162 | IL_53323.1 | 1 | |
| 163 | IL_55649.1 | 1 | |
| 164 | IL_58454.1 | 1 | |
| 165 | IL_63952.1 | 1 | |
| 166 | IL_77296.1 | 1 | |
| 167 | IL_82650.1 | 1 | |
| 168 | IL_86059.1 | 1 | |
| 169 | IL_89794.1 | 1 | |
| 170 | IL_91904.1 | 1 | |
| 171 | IL_95774.1 | 1 | tHS tHH bulge with S-turn |
| 172 | IL_02690.1 | 1 | |
| 173 | IL_04550.1 | 1 | tHS tHH bulge with S-turn |
| 174 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 175 | IL_15674.1 | 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. |
| 176 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 177 | IL_25082.1 | 1 | |
| 178 | IL_37715.1 | 1 | |
| 179 | IL_40845.1 | 1 | |
| 180 | IL_43316.1 | 1 | |
| 181 | IL_64589.1 | 1 | |
| 182 | IL_80505.1 | 1 | |
| 183 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 184 | IL_05221.1 | 1 | |
| 185 | IL_06847.1 | 1 | Group II Intron IL |
| 186 | IL_12486.1 | 1 | |
| 187 | IL_25181.1 | 1 | |
| 188 | IL_28468.1 | 1 | Single sheared with bulged bases |
| 189 | IL_37990.1 | 1 | |
| 190 | IL_46721.1 | 1 | |
| 191 | IL_53988.1 | 1 | |
| 192 | IL_59529.1 | 1 | |
| 193 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 194 | IL_80652.1 | 1 | |
| 195 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 196 | IL_97073.1 | 1 | |
| 197 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 198 | IL_02835.1 | 1 | |
| 199 | IL_05462.1 | 1 | |
| 200 | IL_12507.1 | 1 | |
| 201 | IL_20775.1 | 1 | tSH-inserted |
| 202 | IL_31290.1 | 1 | |
| 203 | IL_41139.1 | 1 | |
| 204 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 205 | IL_78809.1 | 1 | |
| 206 | IL_81398.1 | 1 | |
| 207 | IL_83856.1 | 1 | |
| 208 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 209 | IL_98924.1 | 1 | |
| 210 | IL_02957.1 | 1 | |
| 211 | IL_21221.1 | 1 | SSU Helix 12 (h12) IL |
| 212 | IL_28644.1 | 1 | |
| 213 | IL_34868.1 | 1 | LSU Eukaryal Helix 96 (H96) IL1 |
| 214 | IL_41341.1 | 1 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 215 | IL_47687.1 | 1 | |
| 216 | IL_52509.1 | 1 | |
| 217 | IL_54450.1 | 1 | |
| 218 | IL_56513.1 | 1 | |
| 219 | IL_60643.1 | 1 | |
| 220 | IL_65788.1 | 1 | |
| 221 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 222 | IL_82113.1 | 1 | |
| 223 | IL_83920.1 | 1 | |
| 224 | IL_91044.1 | 1 | |
| 225 | IL_03110.1 | 1 | |
| 226 | IL_06306.1 | 1 | |
| 227 | IL_13434.1 | 1 | |
| 228 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 229 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 230 | IL_39324.1 | 1 | |
| 231 | IL_47732.1 | 1 | |
| 232 | IL_52610.1 | 1 | |
| 233 | IL_54576.1 | 1 | |
| 234 | IL_60649.1 | 1 | Kink-turn |
| 235 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 236 | IL_71942.1 | 1 | |
| 237 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 238 | IL_85510.1 | 1 | |
| 239 | IL_91078.1 | 1 | |
| 240 | IL_92280.1 | 1 | |
| 241 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 242 | IL_03282.1 | 1 | |
| 243 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 244 | IL_11302.1 | 1 | |
| 245 | IL_13682.1 | 1 | |
| 246 | IL_25307.1 | 1 | |
| 247 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 248 | IL_41791.1 | 1 | |
| 249 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 250 | IL_57977.1 | 1 | |
| 251 | IL_61730.1 | 1 | |
| 252 | IL_67735.1 | 1 | |
| 253 | IL_88367.1 | 1 | |
| 254 | IL_91089.1 | 1 | |
| 255 | IL_97842.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_47174.7 | 203 | cWW AG or water inserted cWW Y-Y. |
| 2 | IL_40090.4 | 12 | 16S h34 ILa : Part of larger motif |
Removed motif groups
| # | Motif id | Instances | Description |
|---|
Added motif groups
| # | Motif id | Instances | Description |
|---|