Motif Atlas Releases 1.0 and 1.1
Changes in PDB files used for clustering
Release 1.0 has 200 PDB files, release 1.1 has 200 PDB files, 198 of them are identical.
2 equivalence classes changed representatives: 3ZD3 → 3ZP8, 2ZJR → 4IOA.
No new PDB files have been added.
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 1.0 has 267 motif groups, release 1.1 has 271 motif groups, 179 of them are identical.
51 motif groups were updated, 37 groups are present only in release 1.0, 41 groups are only in release 1.1.
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_31555.3 | 15 | Tandem sheared with inserted, unpaired purine. |
| 2 | IL_02809.2 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 3 | IL_47444.3 | 9 | SRP Loop E-like motif |
| 4 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
| 5 | IL_73000.2 | 7 | cHS-cWS |
| 6 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
| 7 | IL_54420.1 | 6 | |
| 8 | IL_70237.3 | 6 | |
| 9 | IL_77263.1 | 5 | Kink-turn from U4 |
| 10 | IL_25300.1 | 5 | 16S h19 IL and 23S H41 IL |
| 11 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 12 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 13 | IL_78732.3 | 5 | Double S-turn motif |
| 14 | IL_92484.1 | 5 | |
| 15 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 16 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 17 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 18 | IL_71565.2 | 4 | |
| 19 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 20 | IL_39526.4 | 4 | |
| 21 | IL_52173.1 | 3 | |
| 22 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 23 | IL_34628.2 | 3 | Kink-turn |
| 24 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 25 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 26 | IL_95150.3 | 3 | |
| 27 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 28 | IL_05723.1 | 3 | |
| 29 | IL_58586.2 | 3 | |
| 30 | IL_75447.1 | 3 | |
| 31 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 32 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 33 | IL_43946.1 | 3 | |
| 34 | IL_30840.1 | 3 | |
| 35 | IL_89231.1 | 2 | LSU H77 |
| 36 | IL_21495.1 | 2 | |
| 37 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 38 | IL_52940.1 | 2 | |
| 39 | IL_09882.1 | 2 | |
| 40 | IL_77076.1 | 2 | |
| 41 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 42 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 43 | IL_90057.1 | 2 | |
| 44 | IL_46435.1 | 2 | |
| 45 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 46 | IL_37197.1 | 2 | |
| 47 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 48 | IL_01054.1 | 2 | |
| 49 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 50 | IL_16252.3 | 2 | 23S H91 IL |
| 51 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 52 | IL_45794.1 | 2 | |
| 53 | IL_11751.1 | 2 | |
| 54 | IL_97833.1 | 2 | |
| 55 | IL_00998.1 | 2 | |
| 56 | IL_27892.1 | 2 | |
| 57 | IL_07300.1 | 2 | |
| 58 | IL_16330.1 | 2 | |
| 59 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 60 | IL_98566.1 | 2 | |
| 61 | IL_12211.1 | 2 | |
| 62 | IL_55287.1 | 2 | |
| 63 | IL_40892.1 | 2 | |
| 64 | IL_96446.1 | 2 | |
| 65 | IL_50521.1 | 2 | |
| 66 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 67 | IL_37406.1 | 2 | |
| 68 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 69 | IL_87548.1 | 2 | |
| 70 | IL_80093.1 | 2 | |
| 71 | IL_28942.1 | 2 | |
| 72 | IL_23414.1 | 2 | |
| 73 | IL_63952.1 | 1 | |
| 74 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 75 | IL_03110.1 | 1 | |
| 76 | IL_68827.1 | 1 | Reverse Kink-Turn |
| 77 | IL_83920.1 | 1 | |
| 78 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 79 | IL_05462.1 | 1 | |
| 80 | IL_97073.1 | 1 | |
| 81 | IL_02690.1 | 1 | |
| 82 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 83 | IL_82113.1 | 1 | |
| 84 | IL_98924.1 | 1 | |
| 85 | IL_59529.1 | 1 | |
| 86 | IL_17603.1 | 1 | |
| 87 | IL_88367.1 | 1 | |
| 88 | IL_60649.1 | 1 | Kink-turn |
| 89 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 90 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 91 | IL_47687.1 | 1 | |
| 92 | IL_31006.1 | 1 | tSH-tHW-L-bif-cWW |
| 93 | IL_80652.1 | 1 | |
| 94 | IL_12486.1 | 1 | |
| 95 | IL_03741.1 | 1 | |
| 96 | IL_25082.1 | 1 | |
| 97 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 98 | IL_25181.1 | 1 | |
| 99 | IL_56513.1 | 1 | |
| 100 | IL_40527.1 | 1 | Kink-turn |
| 101 | IL_77296.1 | 1 | |
| 102 | IL_39324.1 | 1 | |
| 103 | IL_89794.1 | 1 | |
| 104 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 105 | IL_37715.1 | 1 | |
| 106 | IL_54450.1 | 1 | |
| 107 | IL_77014.1 | 1 | |
| 108 | IL_91078.1 | 1 | |
| 109 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 110 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 111 | IL_21421.1 | 1 | |
| 112 | IL_41139.1 | 1 | |
| 113 | IL_03282.1 | 1 | |
| 114 | IL_88865.1 | 1 | |
| 115 | IL_86059.1 | 1 | |
| 116 | IL_12507.1 | 1 | |
| 117 | IL_53988.1 | 1 | |
| 118 | IL_52509.1 | 1 | |
| 119 | IL_71942.1 | 1 | |
| 120 | IL_67735.1 | 1 | |
| 121 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 122 | IL_37990.1 | 1 | |
| 123 | IL_58454.1 | 1 | |
| 124 | IL_91089.1 | 1 | |
| 125 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 126 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 127 | IL_41791.1 | 1 | |
| 128 | IL_43316.1 | 1 | |
| 129 | IL_80505.1 | 1 | |
| 130 | IL_26868.1 | 1 | |
| 131 | IL_11778.1 | 1 | |
| 132 | IL_27243.1 | 1 | |
| 133 | IL_75328.1 | 1 | |
| 134 | IL_97842.1 | 1 | |
| 135 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 136 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 137 | IL_23448.1 | 1 | |
| 138 | IL_57285.1 | 1 | |
| 139 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 140 | IL_82650.1 | 1 | |
| 141 | IL_11302.1 | 1 | |
| 142 | IL_52958.1 | 1 | |
| 143 | IL_20775.1 | 1 | tSH-inserted |
| 144 | IL_65788.1 | 1 | |
| 145 | IL_61730.1 | 1 | |
| 146 | IL_06306.1 | 1 | |
| 147 | IL_37347.1 | 1 | |
| 148 | IL_46306.1 | 1 | |
| 149 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 150 | IL_60643.1 | 1 | |
| 151 | IL_40845.1 | 1 | |
| 152 | IL_92280.1 | 1 | |
| 153 | IL_57977.1 | 1 | |
| 154 | IL_02835.1 | 1 | |
| 155 | IL_25307.1 | 1 | |
| 156 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 157 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 158 | IL_03931.1 | 1 | 16S h19 IL and 23S H41 IL |
| 159 | IL_78809.1 | 1 | |
| 160 | IL_13682.1 | 1 | |
| 161 | IL_83856.1 | 1 | |
| 162 | IL_05221.1 | 1 | |
| 163 | IL_06471.1 | 1 | |
| 164 | IL_91904.1 | 1 | |
| 165 | IL_15205.1 | 1 | |
| 166 | IL_91044.1 | 1 | |
| 167 | IL_27668.1 | 1 | |
| 168 | IL_85805.1 | 1 | |
| 169 | IL_76263.1 | 1 | |
| 170 | IL_91379.1 | 1 | |
| 171 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 172 | IL_55649.1 | 1 | |
| 173 | IL_54576.1 | 1 | |
| 174 | IL_81398.1 | 1 | |
| 175 | IL_53323.1 | 1 | |
| 176 | IL_26971.1 | 1 | |
| 177 | IL_02957.1 | 1 | |
| 178 | IL_85510.1 | 1 | |
| 179 | IL_06847.1 | 1 | Group II Intron IL |
Updated 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_47174.6 | 201 | cWW AG or water inserted cWW Y-Y. |
| 3 | IL_39199.3 | 54 | Hoogsteen-edge Platform, Single bulged base |
| 4 | IL_41766.3 | 49 | Tandem cWW pairs (Not AU or GC) |
| 5 | IL_56465.3 | 46 | Single, unpaired intercalated base, consensus A |
| 6 | IL_44540.3 | 43 | Sugar-edge, 1-base platform, consensus tHS |
| 7 | IL_87904.4 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
| 8 | IL_06390.3 | 26 | cWH basepair with syn base |
| 9 | IL_13959.3 | 24 | Double Sheared (tSH-tHS) |
| 10 | IL_65553.5 | 22 | Kink-turn |
| 11 | IL_93424.3 | 22 | tSH-inserted-tHW |
| 12 | IL_73276.2 | 20 | C-loop |
| 13 | IL_55938.3 | 18 | LSU Helix 89 (H89) IL2. cSH Platform. |
| 14 | IL_92027.3 | 17 | 16S h21 S8 binding site |
| 15 | IL_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
| 16 | IL_24982.4 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
| 17 | IL_94430.4 | 15 | 16S h32-h33-h34 3WJ |
| 18 | IL_49493.3 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
| 19 | IL_46648.2 | 11 | 23S H91 IL | Single-Base Intercalation Site |
| 20 | IL_40090.3 | 11 | 16S h34 ILa : Part of larger motif |
| 21 | IL_21304.2 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 22 | IL_24546.3 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 23 | IL_90459.3 | 9 | cWW AG or UU |
| 24 | IL_58291.3 | 9 | Recurrent Sub-motif found in junctions |
| 25 | IL_92321.3 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 26 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 27 | IL_90133.2 | 6 | |
| 28 | IL_97057.3 | 6 | |
| 29 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 30 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 31 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 32 | IL_44067.3 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 33 | IL_45262.3 | 5 | |
| 34 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 35 | IL_02359.3 | 5 | |
| 36 | IL_79083.3 | 5 | |
| 37 | IL_08926.2 | 5 | 23S H91 IL |
| 38 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 39 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 40 | IL_16166.3 | 4 | 23S H91 IL |
| 41 | IL_98591.3 | 4 | |
| 42 | IL_38807.3 | 4 | |
| 43 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 44 | IL_34156.6 | 3 | cWW AG or UU |
| 45 | IL_09520.2 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 46 | IL_98421.3 | 3 | SSU Helix 12 (h12) IL |
| 47 | IL_62499.6 | 3 | |
| 48 | 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. |
| 49 | IL_48918.2 | 3 | Kink-turn variant |
| 50 | IL_23262.4 | 2 | |
| 51 | IL_09348.5 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_91487.1 | 21 | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_06429.3 | 15 | cWW-bulge-cWW |
| 3 | IL_27618.2 | 11 | 23S H73 ILa : Part of larger Motif |
| 4 | IL_10007.2 | 7 | Single sheared with bulged bases |
| 5 | IL_38960.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 6 | IL_01239.1 | 5 | |
| 7 | IL_98556.4 | 4 | |
| 8 | IL_87218.1 | 4 | 23S H91 IL |
| 9 | IL_40387.4 | 4 | LSU Helix 89 (H89) IL2 |
| 10 | IL_53774.1 | 3 | Single sheared with bulged bases |
| 11 | IL_36254.1 | 3 | |
| 12 | IL_57216.1 | 3 | tHS tHH bulge with S-turn |
| 13 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 14 | IL_64648.1 | 2 | tHS tHH bulge with S-turn |
| 15 | IL_42397.1 | 2 | |
| 16 | IL_25174.1 | 2 | |
| 17 | IL_91132.1 | 2 | |
| 18 | IL_79870.1 | 2 | tHS tHH bulge with S-turn |
| 19 | IL_06635.1 | 2 | |
| 20 | IL_81441.1 | 2 | |
| 21 | IL_16377.1 | 2 | |
| 22 | IL_87336.1 | 2 | LSU Eukaryal Helix 96 (H96) IL1 |
| 23 | IL_18755.1 | 1 | |
| 24 | IL_88403.1 | 1 | |
| 25 | IL_22579.1 | 1 | |
| 26 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 27 | IL_90880.1 | 1 | |
| 28 | IL_03914.1 | 1 | |
| 29 | IL_44803.1 | 1 | |
| 30 | IL_77195.1 | 1 | |
| 31 | IL_31241.1 | 1 | |
| 32 | IL_55934.1 | 1 | kink-turn-like |
| 33 | IL_82519.1 | 1 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 34 | IL_98688.1 | 1 | |
| 35 | IL_11869.1 | 1 | |
| 36 | IL_61991.1 | 1 | |
| 37 | IL_63837.1 | 1 | tHS tHH bulge with S-turn |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | IL_28947.1 | 21 | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 2 | IL_92109.1 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
| 3 | IL_43124.1 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
| 4 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 5 | IL_16207.1 | 5 | Single sheared with bulged bases |
| 6 | IL_01080.1 | 4 | |
| 7 | IL_42251.1 | 4 | |
| 8 | IL_08559.1 | 4 | LSU Helix 89 (H89) IL2 |
| 9 | IL_80348.1 | 3 | 23S H91 IL |
| 10 | IL_10647.1 | 3 | tHS tHH bulge with S-turn |
| 11 | IL_56077.1 | 3 | |
| 12 | IL_92267.1 | 3 | 23S H73 ILa : Part of larger Motif |
| 13 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 14 | IL_19898.1 | 2 | |
| 15 | IL_33925.1 | 2 | |
| 16 | IL_09587.1 | 2 | |
| 17 | IL_24358.1 | 2 | |
| 18 | IL_33964.1 | 2 | |
| 19 | IL_88180.1 | 2 | cWW-bulge-cWW |
| 20 | IL_09901.1 | 2 | tHS tHH bulge with S-turn |
| 21 | IL_49550.1 | 2 | tHS tHH bulge with S-turn |
| 22 | IL_91273.1 | 2 | |
| 23 | 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. |
| 24 | IL_30067.1 | 1 | |
| 25 | IL_64589.1 | 1 | |
| 26 | IL_95774.1 | 1 | tHS tHH bulge with S-turn |
| 27 | IL_04550.1 | 1 | tHS tHH bulge with S-turn |
| 28 | IL_30354.1 | 1 | |
| 29 | IL_42891.1 | 1 | |
| 30 | IL_31290.1 | 1 | |
| 31 | IL_09491.1 | 1 | |
| 32 | IL_21221.1 | 1 | SSU Helix 12 (h12) IL |
| 33 | IL_46721.1 | 1 | |
| 34 | IL_87394.1 | 1 | |
| 35 | IL_47732.1 | 1 | |
| 36 | IL_28468.1 | 1 | Single sheared with bulged bases |
| 37 | IL_34868.1 | 1 | LSU Eukaryal Helix 96 (H96) IL1 |
| 38 | IL_28644.1 | 1 | |
| 39 | IL_52610.1 | 1 | |
| 40 | IL_13434.1 | 1 | |
| 41 | IL_41341.1 | 1 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |