Motif Atlas Releases 0.12 and 1.0
Changes in PDB files used for clustering
Release 0.12 has 196 PDB files, release 1.0 has 199 PDB files, 196 of them are identical.
No equivalence class representatives have been replaced.
3 new structures in release 1.0: 3W3S, 4ANG, 4B5R.
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 0.12 has 266 motif groups, release 1.0 has 267 motif groups, 233 of them are identical.
14 motif groups were updated, 19 groups are present only in release 0.12, 20 groups are only in release 1.0.
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_47174.5 | 203 | cWW AG or water inserted cWW Y-Y. |
| 2 | IL_39199.2 | 55 | Hoogsteen-edge Platform, Single bulged base |
| 3 | IL_41766.2 | 49 | Tandem cWW pairs (Not AU or GC) |
| 4 | IL_56465.2 | 45 | Single, unpaired intercalated base, consensus A |
| 5 | IL_44540.2 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 6 | IL_87904.3 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 7 | IL_13959.2 | 24 | Double Sheared (tSH-tHS) |
| 8 | IL_65553.4 | 22 | Kink-turn |
| 9 | IL_93424.2 | 22 | tSH-inserted-tHW |
| 10 | IL_73276.1 | 20 | C-loop |
| 11 | IL_55938.2 | 19 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 12 | IL_92027.2 | 17 | 16S h21 S8 binding site |
| 13 | IL_85647.2 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 14 | IL_94430.3 | 15 | 16S h32-h33-h34 3WJ |
| 15 | IL_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 16 | IL_24982.3 | 15 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 17 | IL_49493.2 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 18 | IL_21304.1 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 19 | IL_40090.2 | 11 | 16S h34 ILa : Part of larger motif |
| 20 | IL_46648.1 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 21 | IL_27618.2 | 11 | 23S H73 ILa : Part of larger Motif |
| 22 | IL_24546.2 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 23 | IL_58291.2 | 9 | Recurrent Sub-motif found in junctions |
| 24 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 25 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 26 | IL_90459.2 | 8 | cWW AG or UU |
| 27 | IL_92321.2 | 8 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 28 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 29 | IL_73000.2 | 7 | cHS-cWS |
| 30 | IL_86357.2 | 7 | LSU Helix 61 IL2 |
| 31 | IL_53635.2 | 6 | LSU Helix 32 (H32) IL |
| 32 | IL_25230.2 | 6 | Bacterial 5S rRNA Loop E |
| 33 | IL_72158.2 | 6 | LSU Helix 62 (H62) IL |
| 34 | IL_54420.1 | 6 | |
| 35 | IL_08926.1 | 6 | 23S H91 IL |
| 36 | IL_97057.2 | 6 | |
| 37 | IL_13069.2 | 6 | LSU 3WJ H32-H33-H35A |
| 38 | IL_70237.3 | 6 | |
| 39 | IL_44067.2 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 40 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 41 | IL_45262.2 | 5 | |
| 42 | IL_90133.1 | 5 | |
| 43 | IL_79083.2 | 5 | |
| 44 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 45 | IL_01239.1 | 5 | |
| 46 | IL_77263.1 | 5 | Kink-turn from U4 |
| 47 | IL_92484.1 | 5 | |
| 48 | IL_02359.2 | 5 | |
| 49 | IL_78732.3 | 5 | Double S-turn motif |
| 50 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 51 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 52 | IL_38807.2 | 4 | |
| 53 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 54 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 55 | IL_98591.2 | 4 | |
| 56 | IL_21333.1 | 4 | tSH-tHW-bulge |
| 57 | IL_40387.4 | 4 | LSU Helix 89 (H89) IL2 |
| 58 | IL_93568.1 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 59 | IL_34363.1 | 3 | Kink-turn from 23S H42 |
| 60 | IL_34628.2 | 3 | Kink-turn |
| 61 | IL_23262.3 | 3 | |
| 62 | IL_30840.1 | 3 | |
| 63 | IL_36254.1 | 3 | |
| 64 | IL_53774.1 | 3 | Single sheared with bulged bases |
| 65 | IL_58586.2 | 3 | |
| 66 | IL_98421.2 | 3 | SSU Helix 12 (h12) IL |
| 67 | IL_16166.2 | 3 | |
| 68 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 69 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 70 | IL_95150.3 | 3 | |
| 71 | IL_52173.1 | 3 | |
| 72 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 73 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 74 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 75 | IL_43946.1 | 3 | |
| 76 | IL_75447.1 | 3 | |
| 77 | IL_25174.1 | 2 | |
| 78 | IL_40892.1 | 2 | |
| 79 | IL_55287.1 | 2 | |
| 80 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 81 | IL_90057.1 | 2 | |
| 82 | IL_97833.1 | 2 | |
| 83 | IL_11751.1 | 2 | |
| 84 | IL_28942.1 | 2 | |
| 85 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 86 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 87 | IL_81441.1 | 2 | |
| 88 | IL_87336.1 | 2 | LSU Eukaryal Helix 96 (H96) IL1 |
| 89 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 90 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 91 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 92 | IL_45794.1 | 2 | |
| 93 | IL_87548.1 | 2 | |
| 94 | IL_00998.1 | 2 | |
| 95 | IL_12211.1 | 2 | |
| 96 | IL_23414.1 | 2 | |
| 97 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 98 | IL_50521.1 | 2 | |
| 99 | IL_77076.1 | 2 | |
| 100 | IL_98566.1 | 2 | |
| 101 | IL_01054.1 | 2 | |
| 102 | IL_07300.1 | 2 | |
| 103 | IL_16330.1 | 2 | |
| 104 | IL_37197.1 | 2 | |
| 105 | IL_46435.1 | 2 | |
| 106 | IL_80093.1 | 2 | |
| 107 | IL_16377.1 | 2 | |
| 108 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 109 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 110 | IL_37406.1 | 2 | |
| 111 | IL_52940.1 | 2 | |
| 112 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 113 | IL_89231.1 | 2 | LSU H77 |
| 114 | IL_09882.1 | 2 | |
| 115 | IL_21495.1 | 2 | |
| 116 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 117 | IL_91132.1 | 2 | |
| 118 | IL_02835.1 | 1 | |
| 119 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 120 | IL_11302.1 | 1 | |
| 121 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 122 | IL_22579.1 | 1 | |
| 123 | IL_37990.1 | 1 | |
| 124 | IL_47687.1 | 1 | |
| 125 | IL_53323.1 | 1 | |
| 126 | IL_63952.1 | 1 | |
| 127 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 128 | IL_81398.1 | 1 | |
| 129 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 130 | IL_91904.1 | 1 | |
| 131 | IL_02957.1 | 1 | |
| 132 | IL_06471.1 | 1 | |
| 133 | IL_15205.1 | 1 | |
| 134 | IL_18755.1 | 1 | |
| 135 | IL_25181.1 | 1 | |
| 136 | IL_41139.1 | 1 | |
| 137 | IL_55649.1 | 1 | |
| 138 | IL_58454.1 | 1 | |
| 139 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 140 | IL_78809.1 | 1 | |
| 141 | IL_83856.1 | 1 | |
| 142 | IL_97842.1 | 1 | |
| 143 | IL_03110.1 | 1 | |
| 144 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 145 | IL_11869.1 | 1 | |
| 146 | IL_20775.1 | 1 | tSH-inserted |
| 147 | IL_55934.1 | 1 | kink-turn-like |
| 148 | IL_71942.1 | 1 | |
| 149 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 150 | IL_82113.1 | 1 | |
| 151 | IL_83920.1 | 1 | |
| 152 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 153 | IL_03282.1 | 1 | |
| 154 | IL_06847.1 | 1 | Group II Intron IL |
| 155 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 156 | IL_39324.1 | 1 | |
| 157 | IL_46306.1 | 1 | |
| 158 | IL_53988.1 | 1 | |
| 159 | IL_59529.1 | 1 | |
| 160 | IL_65788.1 | 1 | |
| 161 | IL_85510.1 | 1 | |
| 162 | IL_90880.1 | 1 | |
| 163 | IL_92280.1 | 1 | |
| 164 | IL_03741.1 | 1 | |
| 165 | IL_12486.1 | 1 | |
| 166 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 167 | IL_25307.1 | 1 | |
| 168 | IL_31241.1 | 1 | |
| 169 | IL_41791.1 | 1 | |
| 170 | IL_60643.1 | 1 | |
| 171 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 172 | IL_77195.1 | 1 | |
| 173 | IL_88367.1 | 1 | |
| 174 | IL_91044.1 | 1 | |
| 175 | IL_05221.1 | 1 | |
| 176 | IL_12507.1 | 1 | |
| 177 | IL_26868.1 | 1 | |
| 178 | IL_37347.1 | 1 | |
| 179 | IL_43316.1 | 1 | |
| 180 | IL_52509.1 | 1 | |
| 181 | IL_54450.1 | 1 | |
| 182 | IL_56513.1 | 1 | |
| 183 | IL_60649.1 | 1 | Kink-turn |
| 184 | IL_67735.1 | 1 | |
| 185 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 186 | IL_85805.1 | 1 | |
| 187 | IL_88403.1 | 1 | |
| 188 | IL_91078.1 | 1 | |
| 189 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 190 | IL_05462.1 | 1 | |
| 191 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 192 | IL_21421.1 | 1 | |
| 193 | IL_26971.1 | 1 | |
| 194 | IL_40527.1 | 1 | Kink-turn |
| 195 | IL_54576.1 | 1 | |
| 196 | IL_61730.1 | 1 | |
| 197 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 198 | IL_77296.1 | 1 | |
| 199 | IL_80505.1 | 1 | |
| 200 | IL_82650.1 | 1 | |
| 201 | IL_86059.1 | 1 | |
| 202 | IL_91089.1 | 1 | |
| 203 | IL_97073.1 | 1 | |
| 204 | IL_98688.1 | 1 | |
| 205 | IL_02690.1 | 1 | |
| 206 | IL_06306.1 | 1 | |
| 207 | IL_13682.1 | 1 | |
| 208 | IL_17603.1 | 1 | |
| 209 | IL_25082.1 | 1 | |
| 210 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 211 | IL_37715.1 | 1 | |
| 212 | IL_40845.1 | 1 | |
| 213 | IL_52958.1 | 1 | |
| 214 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 215 | IL_57977.1 | 1 | |
| 216 | IL_61991.1 | 1 | |
| 217 | IL_80652.1 | 1 | |
| 218 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 219 | IL_89794.1 | 1 | |
| 220 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 221 | IL_98924.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_97217.5 | 239 | 1-3 bulged nucleotides, same chain |
| 2 | IL_06390.2 | 26 | cWH basepair with syn base |
| 3 | IL_06429.3 | 15 | cWW-bulge-cWW |
| 4 | IL_02809.2 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 5 | IL_10007.2 | 7 | Single sheared with bulged bases |
| 6 | IL_39526.4 | 4 | |
| 7 | IL_71565.2 | 4 | |
| 8 | IL_98556.4 | 4 | |
| 9 | IL_62499.5 | 3 | |
| 10 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 11 | IL_09348.4 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 12 | IL_89028.4 | 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. |
| 13 | IL_34156.5 | 2 | cWW AG or UU |
| 14 | IL_16252.3 | 2 | 23S H91 IL |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_32390.2 | 21 | 16S h19 IL and 23S H41 IL |
| 2 | IL_89088.1 | 6 | 16S h19 IL and 23S H41 IL |
| 3 | IL_24022.2 | 6 | |
| 4 | IL_10005.1 | 4 | |
| 5 | IL_62661.2 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 6 | IL_91547.1 | 3 | tHS tHH bulge with S-turn |
| 7 | IL_54965.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. |
| 8 | IL_58811.1 | 2 | |
| 9 | IL_33965.1 | 2 | tHS tHH bulge with S-turn |
| 10 | IL_69901.1 | 2 | |
| 11 | IL_82831.2 | 2 | Kink-turn from 16S H23 |
| 12 | IL_47968.1 | 1 | |
| 13 | IL_87544.1 | 1 | |
| 14 | IL_53423.1 | 1 | |
| 15 | IL_96031.1 | 1 | tHS tHH bulge with S-turn |
| 16 | IL_97961.1 | 1 | |
| 17 | IL_37150.1 | 1 | tHS tHH bulge with S-turn |
| 18 | IL_76256.1 | 1 | |
| 19 | IL_41864.1 | 1 | Part of H71 junction in 23S rRNA from T.th. |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_91487.1 | 21 | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_38960.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 3 | IL_25300.1 | 5 | 16S h19 IL and 23S H41 IL |
| 4 | IL_87218.1 | 4 | 23S H91 IL |
| 5 | IL_05723.1 | 3 | |
| 6 | IL_48918.1 | 3 | Kink-turn variant |
| 7 | IL_57216.1 | 3 | tHS tHH bulge with S-turn |
| 8 | IL_27892.1 | 2 | |
| 9 | IL_64648.1 | 2 | tHS tHH bulge with S-turn |
| 10 | IL_79870.1 | 2 | tHS tHH bulge with S-turn |
| 11 | IL_42397.1 | 2 | |
| 12 | IL_06635.1 | 2 | |
| 13 | IL_09520.1 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 14 | IL_63837.1 | 1 | tHS tHH bulge with S-turn |
| 15 | IL_03914.1 | 1 | |
| 16 | IL_03931.1 | 1 | 16S h19 IL and 23S H41 IL |
| 17 | IL_82519.1 | 1 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 18 | IL_44803.1 | 1 | |
| 19 | IL_11778.1 | 1 | |
| 20 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |