Motif Atlas Releases 1.0 and 1.1
Changes in PDB files used for clustering
Release 1.0 has 199 PDB files, release 1.1 has 199 PDB files, 197 of them are identical.
1 equivalence classes changed representatives: 2ZJR → 4IOA.
1 new structures in release 1.1: 3ZP8.
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_70237.3 | 6 | |
| 8 | IL_54420.1 | 6 | |
| 9 | IL_92484.1 | 5 | |
| 10 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
| 11 | IL_25300.1 | 5 | 16S h19 IL and 23S H41 IL |
| 12 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
| 13 | IL_77263.1 | 5 | Kink-turn from U4 |
| 14 | IL_78732.3 | 5 | Double S-turn motif |
| 15 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
| 16 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
| 17 | IL_71565.2 | 4 | |
| 18 | IL_22732.1 | 4 | tSH-inserted-tHS |
| 19 | IL_39526.4 | 4 | |
| 20 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
| 21 | IL_05723.1 | 3 | |
| 22 | IL_30840.1 | 3 | |
| 23 | IL_75447.1 | 3 | |
| 24 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
| 25 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
| 26 | IL_95150.3 | 3 | |
| 27 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
| 28 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
| 29 | IL_43946.1 | 3 | |
| 30 | IL_52173.1 | 3 | |
| 31 | IL_58586.2 | 3 | |
| 32 | IL_34628.2 | 3 | Kink-turn |
| 33 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
| 34 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
| 35 | IL_28942.1 | 2 | |
| 36 | IL_37197.1 | 2 | |
| 37 | IL_46435.1 | 2 | |
| 38 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
| 39 | IL_09882.1 | 2 | |
| 40 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
| 41 | IL_40892.1 | 2 | |
| 42 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
| 43 | IL_90057.1 | 2 | |
| 44 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
| 45 | IL_98566.1 | 2 | |
| 46 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
| 47 | IL_37406.1 | 2 | |
| 48 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
| 49 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
| 50 | IL_11751.1 | 2 | |
| 51 | IL_16252.3 | 2 | 23S H91 IL |
| 52 | IL_21495.1 | 2 | |
| 53 | IL_80093.1 | 2 | |
| 54 | IL_16330.1 | 2 | |
| 55 | IL_31707.1 | 2 | Vitamin B12 aptamer |
| 56 | IL_50521.1 | 2 | |
| 57 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
| 58 | IL_77076.1 | 2 | |
| 59 | IL_00998.1 | 2 | |
| 60 | IL_12211.1 | 2 | |
| 61 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
| 62 | IL_23414.1 | 2 | |
| 63 | IL_87548.1 | 2 | |
| 64 | IL_01054.1 | 2 | |
| 65 | IL_27892.1 | 2 | |
| 66 | IL_45794.1 | 2 | |
| 67 | IL_07300.1 | 2 | |
| 68 | IL_52940.1 | 2 | |
| 69 | IL_55287.1 | 2 | |
| 70 | IL_89231.1 | 2 | LSU H77 |
| 71 | IL_97833.1 | 2 | |
| 72 | IL_05462.1 | 1 | |
| 73 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
| 74 | IL_13682.1 | 1 | |
| 75 | IL_20775.1 | 1 | tSH-inserted |
| 76 | IL_25181.1 | 1 | |
| 77 | IL_40845.1 | 1 | |
| 78 | IL_52958.1 | 1 | |
| 79 | IL_55649.1 | 1 | |
| 80 | IL_60643.1 | 1 | |
| 81 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
| 82 | IL_82113.1 | 1 | |
| 83 | IL_83920.1 | 1 | |
| 84 | IL_89794.1 | 1 | |
| 85 | IL_97842.1 | 1 | |
| 86 | IL_02835.1 | 1 | |
| 87 | IL_15205.1 | 1 | |
| 88 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
| 89 | IL_37347.1 | 1 | |
| 90 | IL_53323.1 | 1 | |
| 91 | IL_56513.1 | 1 | |
| 92 | IL_60649.1 | 1 | Kink-turn |
| 93 | IL_78809.1 | 1 | |
| 94 | IL_85510.1 | 1 | |
| 95 | IL_02957.1 | 1 | |
| 96 | IL_06306.1 | 1 | |
| 97 | IL_11302.1 | 1 | |
| 98 | IL_21421.1 | 1 | |
| 99 | IL_41139.1 | 1 | |
| 100 | IL_47687.1 | 1 | |
| 101 | IL_53988.1 | 1 | |
| 102 | IL_61730.1 | 1 | |
| 103 | IL_85805.1 | 1 | |
| 104 | IL_91044.1 | 1 | |
| 105 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
| 106 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
| 107 | IL_03110.1 | 1 | |
| 108 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
| 109 | IL_25307.1 | 1 | |
| 110 | IL_37715.1 | 1 | |
| 111 | IL_41791.1 | 1 | |
| 112 | IL_57977.1 | 1 | |
| 113 | IL_63952.1 | 1 | |
| 114 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
| 115 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
| 116 | IL_86059.1 | 1 | |
| 117 | IL_91078.1 | 1 | |
| 118 | IL_98924.1 | 1 | |
| 119 | IL_03282.1 | 1 | |
| 120 | IL_06471.1 | 1 | |
| 121 | IL_11778.1 | 1 | |
| 122 | IL_26868.1 | 1 | |
| 123 | IL_37990.1 | 1 | |
| 124 | IL_43316.1 | 1 | |
| 125 | IL_54450.1 | 1 | |
| 126 | IL_58454.1 | 1 | |
| 127 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
| 128 | IL_82650.1 | 1 | |
| 129 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
| 130 | IL_91089.1 | 1 | |
| 131 | IL_03741.1 | 1 | |
| 132 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
| 133 | IL_26971.1 | 1 | |
| 134 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
| 135 | IL_39324.1 | 1 | |
| 136 | IL_54576.1 | 1 | |
| 137 | IL_65788.1 | 1 | |
| 138 | IL_71942.1 | 1 | |
| 139 | IL_80505.1 | 1 | |
| 140 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
| 141 | IL_91904.1 | 1 | |
| 142 | IL_97073.1 | 1 | |
| 143 | IL_03931.1 | 1 | 16S h19 IL and 23S H41 IL |
| 144 | IL_06847.1 | 1 | Group II Intron IL |
| 145 | IL_12486.1 | 1 | |
| 146 | IL_17603.1 | 1 | |
| 147 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
| 148 | IL_52509.1 | 1 | |
| 149 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
| 150 | IL_59529.1 | 1 | |
| 151 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
| 152 | IL_77296.1 | 1 | |
| 153 | IL_80652.1 | 1 | |
| 154 | IL_88367.1 | 1 | |
| 155 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
| 156 | IL_02690.1 | 1 | |
| 157 | IL_05221.1 | 1 | |
| 158 | IL_12507.1 | 1 | |
| 159 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
| 160 | IL_25082.1 | 1 | |
| 161 | IL_40527.1 | 1 | Kink-turn |
| 162 | IL_46306.1 | 1 | |
| 163 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
| 164 | IL_67735.1 | 1 | |
| 165 | IL_81398.1 | 1 | |
| 166 | IL_83856.1 | 1 | |
| 167 | IL_92280.1 | 1 |
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_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_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_21304.2 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 21 | IL_40090.3 | 11 | 16S h34 ILa : Part of larger motif |
| 22 | IL_24546.3 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
| 23 | IL_58291.3 | 9 | Recurrent Sub-motif found in junctions |
| 24 | IL_90459.3 | 9 | cWW AG or UU |
| 25 | IL_92321.3 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
| 26 | IL_97057.3 | 6 | |
| 27 | IL_90133.2 | 6 | |
| 28 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
| 29 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
| 30 | IL_44067.3 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
| 31 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
| 32 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
| 33 | IL_45262.3 | 5 | |
| 34 | IL_02359.3 | 5 | |
| 35 | IL_08926.2 | 5 | 23S H91 IL |
| 36 | IL_79083.3 | 5 | |
| 37 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
| 38 | IL_16166.3 | 4 | 23S H91 IL |
| 39 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
| 40 | IL_38807.3 | 4 | |
| 41 | IL_21333.2 | 4 | tSH-tHW-bulge |
| 42 | IL_98591.3 | 4 | |
| 43 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
| 44 | IL_34156.6 | 3 | cWW AG or UU |
| 45 | IL_62499.6 | 3 | |
| 46 | 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. |
| 47 | IL_48918.2 | 3 | Kink-turn variant |
| 48 | IL_98421.3 | 3 | SSU Helix 12 (h12) IL |
| 49 | IL_09520.2 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
| 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_79870.1 | 2 | tHS tHH bulge with S-turn |
| 14 | IL_06635.1 | 2 | |
| 15 | IL_81441.1 | 2 | |
| 16 | IL_16377.1 | 2 | |
| 17 | IL_87336.1 | 2 | LSU Eukaryal Helix 96 (H96) IL1 |
| 18 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
| 19 | IL_64648.1 | 2 | tHS tHH bulge with S-turn |
| 20 | IL_42397.1 | 2 | |
| 21 | IL_25174.1 | 2 | |
| 22 | IL_91132.1 | 2 | |
| 23 | IL_31241.1 | 1 | |
| 24 | IL_55934.1 | 1 | kink-turn-like |
| 25 | IL_82519.1 | 1 | Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena |
| 26 | IL_98688.1 | 1 | |
| 27 | IL_11869.1 | 1 | |
| 28 | IL_61991.1 | 1 | |
| 29 | IL_63837.1 | 1 | tHS tHH bulge with S-turn |
| 30 | IL_18755.1 | 1 | |
| 31 | IL_88403.1 | 1 | |
| 32 | IL_22579.1 | 1 | |
| 33 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
| 34 | IL_90880.1 | 1 | |
| 35 | IL_03914.1 | 1 | |
| 36 | IL_44803.1 | 1 | |
| 37 | IL_77195.1 | 1 |
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_92267.1 | 3 | 23S H73 ILa : Part of larger Motif |
| 10 | IL_10647.1 | 3 | tHS tHH bulge with S-turn |
| 11 | IL_56077.1 | 3 | |
| 12 | IL_80348.1 | 3 | 23S H91 IL |
| 13 | IL_09587.1 | 2 | |
| 14 | IL_24358.1 | 2 | |
| 15 | IL_33964.1 | 2 | |
| 16 | IL_49550.1 | 2 | tHS tHH bulge with S-turn |
| 17 | IL_09901.1 | 2 | tHS tHH bulge with S-turn |
| 18 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
| 19 | IL_19898.1 | 2 | |
| 20 | IL_88180.1 | 2 | cWW-bulge-cWW |
| 21 | IL_33925.1 | 2 | |
| 22 | IL_91273.1 | 2 | |
| 23 | IL_28468.1 | 1 | Single sheared with bulged bases |
| 24 | IL_34868.1 | 1 | LSU Eukaryal Helix 96 (H96) IL1 |
| 25 | IL_52610.1 | 1 | |
| 26 | IL_28644.1 | 1 | |
| 27 | IL_95774.1 | 1 | tHS tHH bulge with S-turn |
| 28 | IL_13434.1 | 1 | |
| 29 | IL_41341.1 | 1 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
| 30 | IL_64589.1 | 1 | |
| 31 | 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. |
| 32 | IL_30067.1 | 1 | |
| 33 | IL_04550.1 | 1 | tHS tHH bulge with S-turn |
| 34 | IL_30354.1 | 1 | |
| 35 | IL_31290.1 | 1 | |
| 36 | IL_46721.1 | 1 | |
| 37 | IL_09491.1 | 1 | |
| 38 | IL_21221.1 | 1 | SSU Helix 12 (h12) IL |
| 39 | IL_47732.1 | 1 |