Motif Atlas Releases 1.11 and 1.12
Changes in PDB files used for clustering
Release 1.11 has 213 PDB files, release 1.12 has 217 PDB files, 213 of them are identical.
No equivalence class representatives have been replaced.
4 new structures in release 1.12: 4C4W, 4J39, 4J5V, 4OO8.
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 1.11 has 275 motif groups, release 1.12 has 276 motif groups, 253 of them are identical.
11 motif groups were updated, 11 groups are present only in release 1.11, 12 groups are only in release 1.12.
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_97217.10 | 248 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_41766.6 | 54 | Tandem cWW pairs (Not AU or GC) |
| 3 | IL_39199.4 | 53 | Hoogsteen-edge Platform, Single bulged base |
| 4 | IL_56465.4 | 47 | Single, unpaired intercalated base, consensus A |
| 5 | IL_44540.4 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 6 | IL_87904.5 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 7 | 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 |
| 8 | IL_13959.4 | 26 | Double Sheared (tSH-tHS) |
| 9 | 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 |
| 10 | IL_73276.5 | 22 | C-loop |
| 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_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 15 | IL_94430.5 | 16 | 16S h32-h33-h34 3WJ |
| 16 | IL_24982.5 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 17 | IL_46648.6 | 13 | 23S H91 IL | Single-Base Intercalation Site |
| 18 | IL_31555.5 | 13 | Tandem sheared with inserted, unpaired purine. |
| 19 | IL_49493.4 | 13 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 20 | IL_43124.2 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 21 | IL_24546.4 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 22 | IL_58291.4 | 10 | Recurrent Sub-motif found in junctions |
| 23 | IL_90459.3 | 9 | cWW AG or UU |
| 24 | IL_02809.3 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 25 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 26 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 27 | IL_92321.4 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 28 | 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. |
| 29 | IL_73000.2 | 7 | cHS-cWS |
| 30 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 31 | 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) |
| 32 | IL_97057.3 | 6 | |
| 33 | IL_70237.3 | 6 | |
| 34 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 35 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 36 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 37 | IL_08926.3 | 6 | 23S H91 IL |
| 38 | IL_25380.1 | 6 | LSU Helix 89 (H89) IL2 |
| 39 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 40 | IL_77263.2 | 6 | Kink-turn from U4 |
| 41 | IL_90133.3 | 6 | |
| 42 | IL_02359.3 | 5 | |
| 43 | IL_79083.3 | 5 | |
| 44 | IL_44067.4 | 5 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 45 | IL_05684.1 | 5 | tHS tHH bulge with S-turn | Double S-turn motif |
| 46 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 47 | IL_09530.1 | 4 | Double S-turn motif |
| 48 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 49 | IL_28572.2 | 4 | 16S h18 kink-turn like motif |
| 50 | IL_98591.3 | 4 | |
| 51 | IL_31663.1 | 4 | 23S H73 ILa : Part of larger Motif |
| 52 | IL_39526.4 | 4 | |
| 53 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 54 | IL_45262.4 | 4 | |
| 55 | IL_94403.5 | 4 | LSU H77 |
| 56 | IL_97296.1 | 4 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 57 | IL_39980.1 | 4 | |
| 58 | IL_42251.1 | 4 | |
| 59 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 60 | IL_47758.2 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 61 | IL_38807.3 | 4 | |
| 62 | IL_48918.3 | 4 | Kink-turn variant |
| 63 | IL_01080.1 | 4 | |
| 64 | IL_31066.3 | 4 | SSU Helix 44 (h44) extension |
| 65 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 66 | IL_54966.1 | 4 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 67 | IL_82188.2 | 4 | LSU H68 IL from H.m. |
| 68 | IL_95652.3 | 4 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 69 | IL_28003.1 | 3 | |
| 70 | IL_34628.2 | 3 | Kink-turn |
| 71 | IL_43946.1 | 3 | |
| 72 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 73 | IL_35043.1 | 3 | cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base |
| 74 | IL_58586.2 | 3 | |
| 75 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 76 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 77 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 78 | IL_05723.1 | 3 | |
| 79 | IL_25271.2 | 3 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 80 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 81 | IL_07300.2 | 3 | |
| 82 | IL_16166.4 | 3 | 23S H91 IL |
| 83 | IL_52173.1 | 3 | |
| 84 | 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. |
| 85 | IL_06180.1 | 3 | tHS tHH bulge with S-turn |
| 86 | IL_87065.1 | 3 | 23S H91 IL | Single-Base Intercalation Site |
| 87 | IL_16415.2 | 3 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 88 | IL_30840.2 | 3 | |
| 89 | IL_62499.7 | 3 | |
| 90 | IL_98421.4 | 3 | SSU Helix 12 (h12) IL |
| 91 | IL_21639.1 | 2 | |
| 92 | IL_87548.1 | 2 | |
| 93 | IL_98566.1 | 2 | |
| 94 | IL_09587.1 | 2 | |
| 95 | IL_39355.1 | 2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1 |
| 96 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 97 | IL_90735.1 | 2 | |
| 98 | IL_09882.1 | 2 | |
| 99 | IL_50521.1 | 2 | |
| 100 | IL_70401.1 | 2 | |
| 101 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 102 | IL_80093.1 | 2 | |
| 103 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 104 | IL_23262.4 | 2 | |
| 105 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 106 | IL_37197.1 | 2 | |
| 107 | IL_67887.1 | 2 | |
| 108 | IL_11751.1 | 2 | |
| 109 | IL_23414.1 | 2 | |
| 110 | IL_45794.1 | 2 | |
| 111 | IL_77076.1 | 2 | |
| 112 | IL_97509.1 | 2 | Double sheared with wobble cWW. |
| 113 | IL_16330.1 | 2 | |
| 114 | IL_30381.1 | 2 | tHS tHH bulge with S-turn |
| 115 | IL_33842.1 | 2 | |
| 116 | IL_37406.1 | 2 | |
| 117 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 118 | IL_69106.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 119 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 120 | IL_97833.1 | 2 | |
| 121 | IL_00998.1 | 2 | |
| 122 | IL_12211.1 | 2 | |
| 123 | IL_33964.1 | 2 | |
| 124 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 125 | IL_87507.1 | 2 | tHS tHH bulge with S-turn |
| 126 | IL_90057.1 | 2 | |
| 127 | IL_21495.1 | 2 | |
| 128 | IL_40892.1 | 2 | |
| 129 | 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) |
| 130 | IL_46435.1 | 2 | |
| 131 | IL_52940.1 | 2 | |
| 132 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 133 | IL_05221.1 | 1 | |
| 134 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 135 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 136 | IL_25082.1 | 1 | |
| 137 | IL_31224.1 | 1 | 23S H91 IL |
| 138 | IL_39324.1 | 1 | |
| 139 | IL_41139.1 | 1 | |
| 140 | IL_49527.1 | 1 | |
| 141 | IL_52958.1 | 1 | |
| 142 | IL_55649.1 | 1 | |
| 143 | IL_58454.1 | 1 | |
| 144 | IL_64589.1 | 1 | |
| 145 | IL_05513.1 | 1 | |
| 146 | IL_06471.1 | 1 | |
| 147 | IL_18675.1 | 1 | cWW-bulge-cWW |
| 148 | IL_25181.1 | 1 | |
| 149 | IL_41153.1 | 1 | |
| 150 | IL_46721.1 | 1 | |
| 151 | IL_49976.1 | 1 | |
| 152 | IL_53323.1 | 1 | |
| 153 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 154 | IL_85805.1 | 1 | |
| 155 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 156 | IL_02835.1 | 1 | |
| 157 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 158 | IL_15205.1 | 1 | |
| 159 | IL_20775.1 | 1 | tSH-inserted |
| 160 | IL_22909.1 | 1 | |
| 161 | IL_28644.1 | 1 | |
| 162 | IL_59529.1 | 1 | |
| 163 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 164 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 165 | IL_86059.1 | 1 | |
| 166 | IL_88119.1 | 1 | |
| 167 | IL_91044.1 | 1 | |
| 168 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 169 | 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. |
| 170 | IL_06847.1 | 1 | Group II Intron IL |
| 171 | IL_11302.1 | 1 | |
| 172 | IL_21077.1 | 1 | |
| 173 | IL_41791.1 | 1 | |
| 174 | IL_47687.1 | 1 | |
| 175 | IL_50911.1 | 1 | 16S h34 ILa : Part of larger motif |
| 176 | IL_53988.1 | 1 | |
| 177 | IL_56513.1 | 1 | |
| 178 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 179 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 180 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 181 | IL_82650.1 | 1 | |
| 182 | IL_88367.1 | 1 | |
| 183 | IL_91078.1 | 1 | |
| 184 | IL_98924.1 | 1 | |
| 185 | IL_02957.1 | 1 | |
| 186 | IL_06177.1 | 1 | cWW AG or UU |
| 187 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 188 | IL_25307.1 | 1 | |
| 189 | IL_30067.1 | 1 | |
| 190 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 191 | IL_37347.1 | 1 | |
| 192 | IL_47732.1 | 1 | |
| 193 | IL_54450.1 | 1 | |
| 194 | IL_57364.1 | 1 | LSU Helix 89 (H89) IL2 |
| 195 | IL_60649.1 | 1 | Kink-turn |
| 196 | IL_68767.1 | 1 | |
| 197 | IL_71942.1 | 1 | |
| 198 | IL_80505.1 | 1 | |
| 199 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 200 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 201 | IL_91089.1 | 1 | |
| 202 | IL_99397.1 | 1 | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 203 | IL_03110.1 | 1 | |
| 204 | IL_11778.1 | 1 | |
| 205 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 206 | IL_40527.1 | 1 | Kink-turn |
| 207 | IL_52509.1 | 1 | |
| 208 | IL_54470.1 | 1 | tHS tHH bulge with S-turn |
| 209 | IL_61730.1 | 1 | |
| 210 | IL_80652.1 | 1 | |
| 211 | IL_83856.1 | 1 | |
| 212 | IL_89794.1 | 1 | |
| 213 | IL_91904.1 | 1 | |
| 214 | IL_03282.1 | 1 | |
| 215 | IL_06306.1 | 1 | |
| 216 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 217 | IL_21421.1 | 1 | |
| 218 | IL_26868.1 | 1 | |
| 219 | IL_40845.1 | 1 | |
| 220 | IL_43316.1 | 1 | |
| 221 | IL_46306.1 | 1 | |
| 222 | IL_52610.1 | 1 | |
| 223 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 224 | IL_57977.1 | 1 | |
| 225 | IL_77296.1 | 1 | |
| 226 | IL_81398.1 | 1 | |
| 227 | IL_83920.1 | 1 | |
| 228 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 229 | IL_97842.1 | 1 | |
| 230 | IL_03741.1 | 1 | |
| 231 | IL_06421.1 | 1 | Single sheared with bulged bases |
| 232 | IL_09491.1 | 1 | |
| 233 | IL_12507.1 | 1 | |
| 234 | IL_17603.1 | 1 | |
| 235 | IL_26971.1 | 1 | |
| 236 | IL_63952.1 | 1 | |
| 237 | IL_69799.1 | 1 | |
| 238 | IL_85510.1 | 1 | |
| 239 | IL_87523.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_47174.10 | 214 | cWW AG or water inserted cWW Y-Y. |
| 2 | IL_65553.8 | 23 | Kink-turn |
| 3 | IL_92109.3 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 4 | 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) |
| 5 | 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 |
| 6 | IL_25300.3 | 7 | 16S h19 IL and 23S H41 IL |
| 7 | IL_80348.3 | 3 | 23S H91 IL |
| 8 | IL_06211.3 | 3 | |
| 9 | IL_95150.6 | 3 | |
| 10 | IL_96206.3 | 2 | |
| 11 | IL_46034.3 | 2 |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_31473.1 | 2 | |
| 2 | IL_47475.1 | 2 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 3 | IL_74214.1 | 2 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 4 | IL_85015.1 | 2 | 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) |
| 5 | IL_22358.1 | 2 | |
| 6 | IL_95884.1 | 2 | |
| 7 | IL_30354.1 | 1 | |
| 8 | IL_95980.1 | 1 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 9 | IL_34076.1 | 1 | |
| 10 | IL_91956.1 | 1 | |
| 11 | IL_27503.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | 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 |
| 2 | IL_21644.1 | 2 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 3 | 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) |
| 4 | IL_31039.1 | 2 | |
| 5 | IL_46990.1 | 2 | |
| 6 | IL_12024.1 | 2 | |
| 7 | IL_80714.1 | 1 | |
| 8 | IL_86336.1 | 1 | |
| 9 | IL_63253.1 | 1 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 10 | IL_70299.1 | 1 | |
| 11 | IL_13777.1 | 1 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 12 | IL_78513.1 | 1 |