Motif Atlas Releases 1.14 and 1.15
Changes in PDB files used for clustering
Release 1.14 has 236 PDB files, release 1.15 has 245 PDB files, 236 of them are identical.
No equivalence class representatives have been replaced.
9 new structures in release 1.15: 4CUV, 4CUX, 4KR2, 4L81, 4O26, 4P5J, 4P8Z, 4P9R, 4PQV.
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 1.14 has 264 motif groups, release 1.15 has 285 motif groups, 184 of them are identical.
51 motif groups were updated, 29 groups are present only in release 1.14, 50 groups are only in release 1.15.
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 | HL_48039.2 | 11 | MS2 virus RNA Hairpin |
| 2 | HL_17723.5 | 10 | LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot. |
| 3 | HL_15603.2 | 9 | U1A protein-binding Hairpin Loop. |
| 4 | HL_24544.3 | 8 | LSU Helix 53 (H53) Hairpin Loop. T-loop like. |
| 5 | HL_42677.2 | 7 | |
| 6 | HL_62228.4 | 6 | LSU Helix 35A (H35A) Hairpin Loop |
| 7 | HL_57514.2 | 6 | Two base, cross-stacked hairpin loop |
| 8 | HL_06643.3 | 6 | tRNA D-loop. Sec tRNA |
| 9 | HL_89236.1 | 6 | LSU Helix 69 (H69) Hairpin Loop |
| 10 | HL_86077.1 | 5 | GNRA with one bulged base | GNRA-like with bulged base. |
| 11 | HL_45018.3 | 5 | Hairpin-Hairpin Interacting HL |
| 12 | HL_95720.1 | 5 | Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 13 | HL_66174.1 | 5 | cHS GU/cWS Double Platform creates Intercalation site |
| 14 | HL_72273.1 | 5 | tRNA D-loop |
| 15 | HL_78731.2 | 5 | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot |
| 16 | HL_86115.1 | 4 | |
| 17 | HL_62881.1 | 4 | RNase P Structured Hairpin Loop |
| 18 | HL_11376.1 | 4 | LSU Helix 8 (H8) Hairpin Loop |
| 19 | HL_25124.2 | 4 | tSW GA closed tetraloops |
| 20 | HL_61547.5 | 4 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 21 | HL_82418.1 | 4 | LSU Helix 8 (H8) Hairpin Loop |
| 22 | HL_48116.3 | 4 | GNRA-like with 5'-stacking of first unpaired base. |
| 23 | HL_98523.2 | 4 | GNRA-like. Closed by tSH UC. |
| 24 | HL_06997.2 | 3 | |
| 25 | HL_98833.3 | 3 | |
| 26 | HL_41827.1 | 3 | |
| 27 | HL_76766.4 | 3 | |
| 28 | HL_78361.1 | 3 | |
| 29 | HL_33875.1 | 3 | SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like. |
| 30 | HL_19221.2 | 3 | |
| 31 | HL_27429.4 | 3 | |
| 32 | HL_35619.3 | 3 | |
| 33 | HL_91693.2 | 3 | |
| 34 | HL_21545.2 | 3 | LSU Helix 96 (H96) Hairpin Loop |
| 35 | HL_64371.3 | 3 | SSU Central Pseudoknot (forms helix 2) |
| 36 | HL_80492.2 | 3 | tRNA D-loop |
| 37 | HL_13707.2 | 3 | cSH AA Platform containing Hairpin Loop |
| 38 | HL_65924.1 | 2 | |
| 39 | HL_49210.1 | 2 | |
| 40 | HL_78660.1 | 2 | |
| 41 | HL_33451.1 | 2 | |
| 42 | HL_38964.1 | 2 | LSU Helix 84 (H84) Hairpin Loop. E.coli. |
| 43 | HL_42077.3 | 2 | LSU Helix 28 (H28) Hairpin Loop |
| 44 | HL_23290.1 | 2 | |
| 45 | HL_38130.2 | 2 | |
| 46 | HL_94578.1 | 2 | |
| 47 | HL_94309.1 | 2 | GNRA with one bulged base |
| 48 | HL_86123.2 | 2 | SSU Helix 42 (h42) Hairpin Loop. T-loop like. |
| 49 | HL_42094.1 | 2 | |
| 50 | HL_50312.1 | 2 | |
| 51 | HL_87554.1 | 2 | |
| 52 | HL_05361.1 | 2 | |
| 53 | HL_23129.1 | 2 | |
| 54 | HL_24711.1 | 2 | |
| 55 | HL_26495.1 | 2 | |
| 56 | HL_53745.1 | 2 | |
| 57 | HL_19399.1 | 2 | |
| 58 | HL_19528.1 | 2 | |
| 59 | HL_93771.1 | 2 | tRNA T-loop distorted by RS binding |
| 60 | HL_98577.1 | 2 | |
| 61 | HL_42436.1 | 2 | Kissing Hairpin from di-GMP-II riboswitch |
| 62 | HL_91872.1 | 2 | |
| 63 | HL_24473.3 | 2 | tRNA D-loop |
| 64 | HL_42553.1 | 2 | |
| 65 | HL_92635.1 | 2 | |
| 66 | HL_44467.1 | 2 | |
| 67 | HL_25197.1 | 1 | |
| 68 | HL_48480.1 | 1 | |
| 69 | HL_00721.1 | 1 | |
| 70 | HL_26579.1 | 1 | |
| 71 | HL_27397.1 | 1 | |
| 72 | HL_56809.1 | 1 | |
| 73 | HL_67761.1 | 1 | |
| 74 | HL_47337.1 | 1 | |
| 75 | HL_99207.1 | 1 | Tetrahymena LSU hairpin poorly modeled |
| 76 | HL_17537.1 | 1 | |
| 77 | HL_59225.1 | 1 | |
| 78 | HL_59982.1 | 1 | |
| 79 | HL_93428.1 | 1 | |
| 80 | HL_82622.1 | 1 | SSU Central Pseudoknot (forms helix 2) |
| 81 | HL_99779.1 | 1 | |
| 82 | HL_37962.1 | 1 | |
| 83 | HL_63997.1 | 1 | |
| 84 | HL_44522.1 | 1 | |
| 85 | HL_84289.1 | 1 | |
| 86 | HL_12706.1 | 1 | |
| 87 | HL_13786.1 | 1 | |
| 88 | HL_25175.1 | 1 | |
| 89 | HL_97784.1 | 1 | |
| 90 | HL_85018.1 | 1 | |
| 91 | HL_99584.1 | 1 | |
| 92 | HL_29196.1 | 1 | |
| 93 | HL_10894.1 | 1 | |
| 94 | HL_55202.1 | 1 | U2B"-U2A" binding hairpin loop |
| 95 | HL_84768.1 | 1 | |
| 96 | HL_77692.1 | 1 | tRNA D-loop |
| 97 | HL_27236.1 | 1 | |
| 98 | HL_93567.1 | 1 | |
| 99 | HL_57923.1 | 1 | |
| 100 | HL_57217.1 | 1 | cHS platform Intercalation Site |
| 101 | HL_39422.1 | 1 | |
| 102 | HL_30731.1 | 1 | |
| 103 | HL_70912.1 | 1 | |
| 104 | HL_03785.1 | 1 | LSU Helix 8 (H8) Hairpin Loop |
| 105 | HL_78228.1 | 1 | |
| 106 | HL_10116.1 | 1 | Kink-turn-like Hairpin Loop |
| 107 | HL_19452.1 | 1 | tRNA D-loop |
| 108 | HL_08203.1 | 1 | |
| 109 | HL_96012.1 | 1 | |
| 110 | HL_38898.1 | 1 | |
| 111 | HL_38138.1 | 1 | |
| 112 | HL_10075.1 | 1 | |
| 113 | HL_45411.1 | 1 | |
| 114 | HL_30366.1 | 1 | LSU Helix 10 (H10) Hairpin E.coli |
| 115 | HL_52540.1 | 1 | |
| 116 | HL_79902.1 | 1 | |
| 117 | HL_68579.1 | 1 | |
| 118 | HL_62880.1 | 1 | |
| 119 | HL_95716.1 | 1 | |
| 120 | HL_46570.1 | 1 | |
| 121 | HL_98233.1 | 1 | |
| 122 | HL_30008.1 | 1 | |
| 123 | HL_23080.1 | 1 | |
| 124 | HL_17008.1 | 1 | Nova-2 KH3 domain binding hairpin |
| 125 | HL_56775.1 | 1 | |
| 126 | HL_52116.1 | 1 | |
| 127 | HL_65802.1 | 1 | |
| 128 | HL_99612.1 | 1 | |
| 129 | HL_50018.1 | 1 | |
| 130 | HL_53789.1 | 1 | |
| 131 | HL_19226.1 | 1 | |
| 132 | HL_95049.1 | 1 | Two base, cross-stacked hairpin loop |
| 133 | HL_05113.1 | 1 | |
| 134 | HL_19132.1 | 1 | |
| 135 | HL_91613.1 | 1 | |
| 136 | HL_55272.1 | 1 | |
| 137 | HL_93530.1 | 1 | |
| 138 | HL_83865.1 | 1 | |
| 139 | HL_73465.1 | 1 | |
| 140 | HL_42345.1 | 1 | |
| 141 | HL_20920.1 | 1 | |
| 142 | HL_73972.1 | 1 | |
| 143 | HL_46055.1 | 1 | |
| 144 | HL_85044.1 | 1 | LSU Helix 10 (H10) Hairpin E.coli |
| 145 | HL_25195.1 | 1 | |
| 146 | HL_45358.1 | 1 | Double hairpin loop based on GGA triple |
| 147 | HL_84888.1 | 1 | T-loop like but without tWH UA |
| 148 | HL_88960.1 | 1 | |
| 149 | HL_67000.1 | 1 | |
| 150 | HL_53015.1 | 1 | |
| 151 | HL_82243.1 | 1 | |
| 152 | HL_23195.1 | 1 | |
| 153 | HL_79038.1 | 1 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 154 | HL_96994.1 | 1 | |
| 155 | HL_49998.1 | 1 | |
| 156 | HL_59610.1 | 1 | |
| 157 | HL_38897.1 | 1 | S8 operon binding Hairpin Loop. T-loop like with purine stacking. |
| 158 | HL_35865.1 | 1 | |
| 159 | HL_99932.1 | 1 | |
| 160 | HL_20806.1 | 1 | |
| 161 | HL_60203.1 | 1 | |
| 162 | HL_68435.1 | 1 | |
| 163 | HL_66877.1 | 1 | cSH GU/cWS double platform, intercalation site |
| 164 | HL_93263.1 | 1 | |
| 165 | HL_69403.1 | 1 | GNRA-like |
| 166 | HL_49492.1 | 1 | Forms 7-BP PseudoKnot. Has embedded sarcin-like motif |
| 167 | HL_01418.1 | 1 | |
| 168 | HL_24108.1 | 1 | |
| 169 | HL_85982.1 | 1 | |
| 170 | HL_33640.1 | 1 | |
| 171 | HL_04305.1 | 1 | |
| 172 | HL_24707.1 | 1 | |
| 173 | HL_19363.1 | 1 | |
| 174 | HL_78507.1 | 1 | |
| 175 | HL_87223.1 | 1 | |
| 176 | HL_58223.1 | 1 | |
| 177 | HL_66880.1 | 1 | |
| 178 | HL_44390.1 | 1 | |
| 179 | HL_50059.1 | 1 | LSU Helix 35 (H35) Hairpin Loop from Yeast |
| 180 | HL_82288.1 | 1 | |
| 181 | HL_97022.1 | 1 | |
| 182 | HL_20028.1 | 1 | |
| 183 | HL_59182.1 | 1 | |
| 184 | HL_53116.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_67042.14 | 270 | GNRA Hairpin motifs |
| 2 | HL_72498.14 | 71 | T-loops with two bulged bases |
| 3 | HL_39895.8 | 38 | UNCG Hairpin motifs |
| 4 | HL_18781.6 | 24 | Double sheared (tSH) with U-turn |
| 5 | HL_91226.5 | 20 | Kissing Hairpin motif |
| 6 | HL_97270.5 | 17 | T-loops with 1 bulged base |
| 7 | HL_74465.6 | 16 | tRNA Anti-Codon loop |
| 8 | HL_27271.3 | 14 | LSU Helix 96 (H96) Hairpin Loop |
| 9 | HL_46175.4 | 13 | SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops |
| 10 | HL_49036.5 | 13 | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base |
| 11 | HL_75759.6 | 12 | |
| 12 | HL_56824.4 | 12 | LSU Helix 60A. LSU Helix 63A. |
| 13 | HL_33402.5 | 11 | LSU Helix 13 (H13) Hairpin loop. GNRA-like. |
| 14 | HL_68081.5 | 11 | LSU Helix 20 Hairpin loop |
| 15 | HL_82294.4 | 11 | SSU Helix 37 (h37) Hairpin loop. |
| 16 | HL_80459.5 | 10 | |
| 17 | HL_34027.4 | 9 | 5S Loop C - Upper part of Hairpin Loop. |
| 18 | HL_39942.4 | 8 | LSU Helix 91 (H91) Hairpin Loop |
| 19 | HL_41833.4 | 8 | LSU Helix 81 (H81) Hairpin Loop |
| 20 | HL_11547.4 | 8 | LSU Helix 80 (H80) P-site Hairpin Loop. |
| 21 | HL_46489.4 | 8 | LSU H89 Hairpin Loop |
| 22 | HL_75579.4 | 8 | |
| 23 | HL_87136.4 | 8 | LSU Helix 39A Hairpin loop |
| 24 | HL_18156.4 | 8 | LSU Helix 72 (H72) Hairpin Loop |
| 25 | HL_34108.4 | 8 | LSU Helix 37 (H37) Hairpin Loop. |
| 26 | HL_39872.4 | 8 | LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA. |
| 27 | HL_70420.4 | 8 | LSU Helix 97 Hairpin loop |
| 28 | HL_01926.5 | 8 | LSU Helix 71 (H71) Hairpin Loop. |
| 29 | HL_85534.3 | 7 | LSU Helix 65 (H65) Hairpin Loop. T-loop like. |
| 30 | HL_11509.4 | 7 | LSU Helix 6 (H6) Hairpin Loop. |
| 31 | HL_88311.4 | 7 | LSU Helix 35 (H35) Hairpin Loop |
| 32 | HL_72543.3 | 6 | LSU Helix 43 (H43) Hairpin Loop. T-loop Like. |
| 33 | HL_82538.3 | 6 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 34 | HL_31318.2 | 6 | SSU Central Pseudoknot (forms helix 2) |
| 35 | HL_08382.4 | 5 | |
| 36 | HL_99908.2 | 5 | LSU Helix 69 (H69) Hairpin Loop |
| 37 | HL_64543.3 | 5 | SSU Helix 31 (h31) Hairpin Loop |
| 38 | HL_23182.2 | 4 | |
| 39 | HL_48254.3 | 4 | LSU Helix 84 (H84) Hairpin Loop. |
| 40 | HL_79956.2 | 4 | GNRA-like with 5'-stacking of first unpaired base. |
| 41 | HL_19905.4 | 4 | LSU: Part of IL/3WJ between H55 and H56. |
| 42 | HL_06122.2 | 3 | |
| 43 | HL_58083.3 | 3 | |
| 44 | HL_99633.2 | 3 | |
| 45 | HL_60200.2 | 3 | |
| 46 | HL_74559.2 | 3 | Two base, cross-stacked hairpin loop |
| 47 | HL_86398.2 | 3 | |
| 48 | HL_65249.2 | 3 | |
| 49 | HL_18587.2 | 3 | |
| 50 | HL_54751.3 | 3 | |
| 51 | HL_96915.2 | 3 |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_52574.4 | 15 | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. |
| 2 | HL_87844.3 | 8 | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. |
| 3 | HL_55718.1 | 4 | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56. |
| 4 | HL_84258.1 | 3 | LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 5 | HL_68697.3 | 3 | |
| 6 | HL_16643.1 | 3 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 7 | HL_17790.1 | 2 | UNCG-like. cWW Closing pair. |
| 8 | HL_81510.1 | 2 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 9 | HL_46903.1 | 2 | |
| 10 | HL_50461.1 | 2 | |
| 11 | HL_65347.1 | 2 | SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops |
| 12 | HL_86889.1 | 2 | SSU Central Pseudoknot (forms helix 2) |
| 13 | HL_74505.1 | 2 | |
| 14 | HL_90542.1 | 2 | |
| 15 | HL_62967.1 | 2 | |
| 16 | HL_95756.1 | 2 | |
| 17 | HL_16728.1 | 2 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 18 | HL_63304.1 | 1 | |
| 19 | HL_65071.1 | 1 | |
| 20 | HL_00090.1 | 1 | |
| 21 | HL_04194.1 | 1 | |
| 22 | HL_68733.1 | 1 | LSU Yeast Hairpin Loop |
| 23 | HL_90102.1 | 1 | Kink-turn-like Hairpin Loop |
| 24 | HL_10378.1 | 1 | Double 5'-stacked purine Hairpin Loop from Eukaryal LSU |
| 25 | HL_57843.1 | 1 | |
| 26 | HL_75850.1 | 1 | |
| 27 | HL_62970.1 | 1 | |
| 28 | HL_78420.1 | 1 | |
| 29 | HL_97499.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_92565.1 | 16 | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. |
| 2 | HL_89482.1 | 10 | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop. |
| 3 | HL_25878.1 | 5 | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56. |
| 4 | HL_19626.1 | 5 | LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 5 | HL_92706.1 | 4 | LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 6 | HL_95969.1 | 3 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 7 | HL_74307.1 | 3 | |
| 8 | HL_91142.1 | 3 | Double 5'-stacked purine Hairpin Loop from Eukaryal LSU |
| 9 | HL_19033.1 | 3 | SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops |
| 10 | HL_33223.1 | 3 | SSU Central Pseudoknot (forms helix 2) |
| 11 | HL_55684.1 | 3 | |
| 12 | HL_66677.1 | 3 | |
| 13 | HL_84911.1 | 3 | |
| 14 | HL_84967.1 | 2 | |
| 15 | HL_09641.1 | 2 | SSU Central Pseudoknot (forms helix 2) |
| 16 | HL_41700.1 | 2 | |
| 17 | HL_27478.1 | 2 | |
| 18 | HL_64438.1 | 2 | Kink-turn-like Hairpin Loop |
| 19 | HL_28339.1 | 2 | |
| 20 | HL_64803.1 | 2 | |
| 21 | HL_50937.1 | 2 | |
| 22 | HL_65386.1 | 2 | UNCG-like. cWW Closing pair. |
| 23 | HL_84172.1 | 2 | |
| 24 | HL_20004.1 | 2 | |
| 25 | HL_94189.1 | 2 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 26 | HL_01788.1 | 2 | LSU Yeast Hairpin Loop |
| 27 | HL_34912.1 | 2 | |
| 28 | HL_04979.1 | 1 | LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA. |
| 29 | HL_22461.1 | 1 | |
| 30 | HL_39846.1 | 1 | |
| 31 | HL_62564.1 | 1 | LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 32 | HL_72389.1 | 1 | |
| 33 | HL_22533.1 | 1 | |
| 34 | HL_64102.1 | 1 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 35 | HL_11337.1 | 1 | |
| 36 | HL_42255.1 | 1 | |
| 37 | HL_64209.1 | 1 | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56. |
| 38 | HL_75624.1 | 1 | |
| 39 | HL_90541.1 | 1 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 40 | HL_14536.1 | 1 | |
| 41 | HL_44485.1 | 1 | 16S helix 23 and 24 hairpin loops |
| 42 | HL_75984.1 | 1 | |
| 43 | HL_45740.1 | 1 | |
| 44 | HL_78389.1 | 1 | |
| 45 | HL_34491.1 | 1 | |
| 46 | HL_84720.1 | 1 | |
| 47 | HL_21695.1 | 1 | UNCG-like. cWW Closing pair. |
| 48 | HL_57667.1 | 1 | |
| 49 | HL_70872.1 | 1 | |
| 50 | HL_95079.1 | 1 |