Motif Atlas Releases 1.12 and 1.13
Changes in PDB files used for clustering
Release 1.12 has 231 PDB files, release 1.13 has 231 PDB files, 230 of them are identical.
1 equivalence classes changed representatives: 3SD3 → 4LVZ.
No new PDB files have been added.
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 1.12 has 253 motif groups, release 1.13 has 253 motif groups, 251 of them are identical.
1 motif groups were updated, 1 groups are present only in release 1.12, 1 groups are only in release 1.13.
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_72498.12 | 66 | T-loops with two bulged bases |
| 2 | HL_39895.6 | 35 | UNCG Hairpin motifs |
| 3 | HL_18781.4 | 20 | Double sheared (tSH) with U-turn |
| 4 | HL_91226.3 | 17 | Kissing Hairpin motif |
| 5 | HL_97270.3 | 15 | T-loops with 1 bulged base |
| 6 | HL_52574.3 | 14 | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. |
| 7 | HL_74465.5 | 13 | tRNA Anti-Codon loop |
| 8 | HL_49036.3 | 12 | GNRA with one bulged base |
| 9 | HL_27271.2 | 12 | LSU Helix 96 (H96) Hairpin Loop |
| 10 | HL_48039.2 | 11 | MS2 virus RNA Hairpin |
| 11 | HL_75759.4 | 11 | |
| 12 | HL_17723.4 | 10 | LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot. |
| 13 | HL_68081.3 | 10 | LSU Helix 20 Hairpin loop |
| 14 | HL_46175.2 | 10 | 16S helix 23 and 24 hairpin loops |
| 15 | HL_56824.2 | 10 | LSU Helix 60A. LSU Helix 63A. |
| 16 | HL_15603.2 | 9 | U1A protein-binding Hairpin Loop. |
| 17 | HL_80459.3 | 9 | |
| 18 | HL_87844.2 | 9 | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. |
| 19 | HL_82294.3 | 8 | SSU Helix 37 (h37) Hairpin loop. |
| 20 | HL_33402.3 | 8 | LSU Helix 13 (H13) Hairpin loop. GNRA-like. |
| 21 | HL_34027.2 | 8 | 5S Loop C - Upper part of Hairpin Loop. |
| 22 | HL_11547.2 | 8 | LSU Helix 80 (H80) P-site Hairpin Loop. |
| 23 | HL_24544.2 | 8 | LSU Helix 53 (H53) Hairpin Loop. T-loop like. |
| 24 | HL_42677.2 | 7 | |
| 25 | HL_01926.3 | 6 | LSU Helix 71 (H71) Hairpin Loop. |
| 26 | HL_70420.2 | 6 | LSU Helix 97 Hairpin loop |
| 27 | HL_57514.2 | 6 | Two base, cross-stacked hairpin loop |
| 28 | HL_34108.2 | 6 | LSU Helix 37 (H37) Hairpin Loop. |
| 29 | HL_18156.2 | 6 | LSU Helix 72 (H72) Hairpin Loop |
| 30 | HL_39872.2 | 6 | LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA. |
| 31 | HL_75579.2 | 6 | |
| 32 | HL_87136.2 | 6 | LSU Helix 39A Hairpin loop |
| 33 | HL_11509.2 | 6 | LSU Helix 6 (H6) Hairpin Loop. |
| 34 | HL_41833.2 | 6 | LSU Helix 81 (H81) Hairpin Loop |
| 35 | HL_46489.2 | 6 | LSU H89 Hairpin Loop |
| 36 | HL_39942.2 | 6 | LSU Helix 91 (H91) Hairpin Loop |
| 37 | HL_06643.3 | 6 | tRNA D-loop. Sec tRNA |
| 38 | HL_62228.3 | 5 | LSU Helix 35A (H35A) Hairpin Loop |
| 39 | HL_72273.1 | 5 | tRNA D-loop |
| 40 | HL_78731.1 | 5 | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot |
| 41 | HL_72543.2 | 5 | LSU Helix 43 (H43) Hairpin Loop. T-loop Like. |
| 42 | HL_45018.3 | 5 | Hairpin-Hairpin Interacting HL |
| 43 | HL_82538.1 | 5 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 44 | HL_95720.1 | 5 | Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 45 | HL_88311.2 | 5 | LSU Helix 35 (H35) Hairpin Loop |
| 46 | HL_85534.1 | 5 | LSU Helix 65 (H65) Hairpin Loop. T-loop like. |
| 47 | HL_66174.1 | 5 | cHS GU/cWS Double Platform creates Intercalation site |
| 48 | HL_86115.1 | 4 | |
| 49 | HL_62881.1 | 4 | RNase P Structured Hairpin Loop |
| 50 | HL_29831.1 | 4 | GNRA-like with bulged base. |
| 51 | HL_61547.5 | 4 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 52 | HL_25124.2 | 4 | tSW GA closed tetraloops |
| 53 | HL_55718.1 | 4 | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56. |
| 54 | HL_11376.1 | 4 | LSU Helix 8 (H8) Hairpin Loop |
| 55 | HL_98523.2 | 4 | GNRA-like. Closed by tSH UC. |
| 56 | HL_48116.2 | 4 | GNRA-like with 5'-stacking of first unpaired base. |
| 57 | HL_47784.2 | 4 | SSU Central Pseudoknot (forms helix 2) |
| 58 | HL_64543.2 | 4 | SSU Helix 31 (h31) Hairpin Loop |
| 59 | HL_19221.2 | 3 | |
| 60 | HL_41827.1 | 3 | |
| 61 | HL_98833.3 | 3 | |
| 62 | HL_76036.3 | 3 | LSU Helix 8 (H8) Hairpin Loop |
| 63 | HL_58083.2 | 3 | |
| 64 | HL_74686.1 | 3 | SSU Central Pseudoknot (forms helix 2) |
| 65 | HL_48254.1 | 3 | LSU Helix 84 (H84) Hairpin Loop. |
| 66 | HL_33875.1 | 3 | SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like. |
| 67 | HL_08382.2 | 3 | |
| 68 | HL_42077.2 | 3 | LSU Helix 28 (H28) Hairpin Loop |
| 69 | HL_23182.1 | 3 | |
| 70 | HL_80492.2 | 3 | tRNA D-loop |
| 71 | HL_27429.3 | 3 | |
| 72 | HL_06997.2 | 3 | |
| 73 | HL_19905.3 | 3 | LSU: Part of IL/3WJ between H55 and H56. |
| 74 | HL_35619.2 | 3 | |
| 75 | HL_76766.4 | 3 | |
| 76 | HL_68697.2 | 3 | |
| 77 | HL_13707.2 | 3 | cSH AA Platform containing Hairpin Loop |
| 78 | HL_78361.1 | 3 | |
| 79 | HL_90579.3 | 3 | LSU Helix 69 (H69) Hairpin Loop |
| 80 | HL_74505.1 | 2 | |
| 81 | HL_24473.3 | 2 | tRNA D-loop |
| 82 | HL_65347.1 | 2 | SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops |
| 83 | HL_19399.1 | 2 | |
| 84 | HL_93771.1 | 2 | tRNA T-loop distorted by RS binding |
| 85 | HL_42094.1 | 2 | |
| 86 | HL_99633.1 | 2 | |
| 87 | HL_06122.1 | 2 | |
| 88 | HL_65924.1 | 2 | |
| 89 | HL_86123.2 | 2 | SSU Helix 42 (h42) Hairpin Loop. T-loop like. |
| 90 | HL_17790.1 | 2 | UNCG-like. cWW Closing pair. |
| 91 | HL_05361.1 | 2 | |
| 92 | HL_98577.1 | 2 | |
| 93 | HL_21545.1 | 2 | LSU Helix 96 (H96) Hairpin Loop |
| 94 | HL_84353.1 | 2 | |
| 95 | HL_38130.2 | 2 | |
| 96 | HL_26495.1 | 2 | |
| 97 | HL_87554.1 | 2 | |
| 98 | HL_86398.1 | 2 | |
| 99 | HL_96915.1 | 2 | |
| 100 | HL_66948.1 | 2 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 101 | HL_16770.1 | 2 | |
| 102 | HL_65249.1 | 2 | |
| 103 | HL_19528.1 | 2 | |
| 104 | HL_23129.1 | 2 | |
| 105 | HL_91872.1 | 2 | |
| 106 | HL_42553.1 | 2 | |
| 107 | HL_64371.2 | 2 | |
| 108 | HL_42436.1 | 2 | Kissing Hairpin from di-GMP-II riboswitch |
| 109 | HL_60200.1 | 2 | |
| 110 | HL_24711.1 | 2 | |
| 111 | HL_49210.1 | 2 | |
| 112 | HL_33451.1 | 2 | |
| 113 | HL_50312.1 | 2 | |
| 114 | HL_74559.1 | 2 | Two base, cross-stacked hairpin loop |
| 115 | HL_90542.1 | 2 | |
| 116 | HL_63941.1 | 2 | |
| 117 | HL_54751.2 | 2 | |
| 118 | HL_91693.1 | 2 | |
| 119 | HL_21675.3 | 2 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 120 | HL_23290.1 | 2 | |
| 121 | HL_94578.1 | 2 | |
| 122 | HL_32644.2 | 2 | LSU Helix 69 (H69) Hairpin Loop |
| 123 | HL_44467.1 | 2 | |
| 124 | HL_18587.1 | 2 | |
| 125 | HL_62967.1 | 2 | |
| 126 | HL_52116.1 | 1 | |
| 127 | HL_57923.1 | 1 | |
| 128 | HL_78507.1 | 1 | |
| 129 | HL_45358.1 | 1 | Double hairpin loop based on GGA triple |
| 130 | HL_42969.1 | 1 | |
| 131 | HL_79902.1 | 1 | |
| 132 | HL_30731.1 | 1 | |
| 133 | HL_07915.1 | 1 | |
| 134 | HL_00090.1 | 1 | |
| 135 | HL_10378.1 | 1 | Double 5'-stacked purine Hairpin Loop from Eukaryal LSU |
| 136 | HL_50059.1 | 1 | LSU Helix 35 (H35) Hairpin Loop from Yeast |
| 137 | HL_78228.1 | 1 | |
| 138 | HL_97971.1 | 1 | |
| 139 | HL_69403.1 | 1 | GNRA-like |
| 140 | HL_46570.1 | 1 | |
| 141 | HL_73465.1 | 1 | |
| 142 | HL_42345.1 | 1 | |
| 143 | HL_73972.1 | 1 | |
| 144 | HL_85044.1 | 1 | LSU Helix 10 (H10) Hairpin E.coli |
| 145 | HL_45411.1 | 1 | |
| 146 | HL_94697.1 | 1 | LSU Helix 84 (H84) Hairpin Loop. E.coli. |
| 147 | HL_60203.1 | 1 | |
| 148 | HL_68435.1 | 1 | |
| 149 | HL_84888.1 | 1 | T-loop like but without tWH UA |
| 150 | HL_57843.1 | 1 | |
| 151 | HL_68579.1 | 1 | |
| 152 | HL_12706.1 | 1 | |
| 153 | HL_67761.1 | 1 | |
| 154 | HL_63304.1 | 1 | |
| 155 | HL_75850.1 | 1 | |
| 156 | HL_35200.1 | 1 | |
| 157 | HL_82288.1 | 1 | |
| 158 | HL_83865.1 | 1 | |
| 159 | HL_79038.1 | 1 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 160 | HL_96994.1 | 1 | |
| 161 | HL_84768.1 | 1 | |
| 162 | HL_38897.1 | 1 | S8 operon binding Hairpin Loop. T-loop like with purine stacking. |
| 163 | HL_53789.1 | 1 | |
| 164 | HL_30366.1 | 1 | LSU Helix 10 (H10) Hairpin E.coli |
| 165 | HL_76585.1 | 1 | |
| 166 | HL_87223.1 | 1 | |
| 167 | HL_58223.1 | 1 | |
| 168 | HL_19132.1 | 1 | |
| 169 | HL_70912.1 | 1 | |
| 170 | HL_13786.1 | 1 | |
| 171 | HL_55272.1 | 1 | |
| 172 | HL_47337.1 | 1 | |
| 173 | HL_39486.1 | 1 | |
| 174 | HL_36842.1 | 1 | |
| 175 | HL_23195.1 | 1 | |
| 176 | HL_01418.1 | 1 | |
| 177 | HL_24108.1 | 1 | |
| 178 | HL_55202.1 | 1 | U2B"-U2A" binding hairpin loop |
| 179 | HL_38138.1 | 1 | |
| 180 | HL_24707.1 | 1 | |
| 181 | HL_25195.1 | 1 | |
| 182 | HL_59604.1 | 1 | |
| 183 | HL_97499.1 | 1 | |
| 184 | HL_00721.1 | 1 | |
| 185 | HL_26579.1 | 1 | |
| 186 | HL_58601.1 | 1 | |
| 187 | HL_88960.1 | 1 | |
| 188 | HL_91613.1 | 1 | |
| 189 | HL_53015.1 | 1 | |
| 190 | HL_78420.1 | 1 | |
| 191 | HL_33277.1 | 1 | |
| 192 | HL_49492.1 | 1 | Forms 7-BP PseudoKnot. Has embedded sarcin-like motif |
| 193 | HL_20028.1 | 1 | |
| 194 | HL_59182.1 | 1 | |
| 195 | HL_33640.1 | 1 | |
| 196 | HL_65802.1 | 1 | |
| 197 | HL_35865.1 | 1 | |
| 198 | HL_25197.1 | 1 | |
| 199 | HL_37962.1 | 1 | |
| 200 | HL_65071.1 | 1 | |
| 201 | HL_44522.1 | 1 | |
| 202 | HL_66877.1 | 1 | cSH GU/cWS double platform, intercalation site |
| 203 | HL_03785.1 | 1 | LSU Helix 8 (H8) Hairpin Loop |
| 204 | HL_25175.1 | 1 | |
| 205 | HL_68733.1 | 1 | LSU Yeast Hairpin Loop |
| 206 | HL_66467.1 | 1 | |
| 207 | HL_99207.1 | 1 | Tetrahymena LSU hairpin poorly modeled |
| 208 | HL_17537.1 | 1 | |
| 209 | HL_59225.1 | 1 | |
| 210 | HL_38898.1 | 1 | |
| 211 | HL_59610.1 | 1 | |
| 212 | HL_56775.1 | 1 | |
| 213 | HL_28676.1 | 1 | |
| 214 | HL_57217.1 | 1 | cHS platform Intercalation Site |
| 215 | HL_39422.1 | 1 | |
| 216 | HL_66880.1 | 1 | |
| 217 | HL_67000.1 | 1 | |
| 218 | HL_62970.1 | 1 | |
| 219 | HL_76679.1 | 1 | |
| 220 | HL_90102.1 | 1 | Kink-turn-like Hairpin Loop |
| 221 | HL_97784.1 | 1 | |
| 222 | HL_85018.1 | 1 | |
| 223 | HL_99584.1 | 1 | |
| 224 | HL_29196.1 | 1 | |
| 225 | HL_17008.1 | 1 | Nova-2 KH3 domain binding hairpin |
| 226 | HL_77692.1 | 1 | tRNA D-loop |
| 227 | HL_30128.1 | 1 | |
| 228 | HL_48480.1 | 1 | |
| 229 | HL_20806.1 | 1 | |
| 230 | HL_52540.1 | 1 | |
| 231 | HL_84289.1 | 1 | |
| 232 | HL_27397.1 | 1 | |
| 233 | HL_44390.1 | 1 | |
| 234 | HL_93263.1 | 1 | |
| 235 | HL_62880.1 | 1 | |
| 236 | HL_04194.1 | 1 | |
| 237 | HL_93530.1 | 1 | |
| 238 | HL_19452.1 | 1 | tRNA D-loop |
| 239 | HL_08203.1 | 1 | |
| 240 | HL_93567.1 | 1 | |
| 241 | HL_99779.1 | 1 | |
| 242 | HL_19226.1 | 1 | |
| 243 | HL_95049.1 | 1 | Two base, cross-stacked hairpin loop |
| 244 | HL_05113.1 | 1 | |
| 245 | HL_34440.1 | 1 | |
| 246 | HL_56809.1 | 1 | |
| 247 | HL_95716.1 | 1 | |
| 248 | HL_82243.1 | 1 | |
| 249 | HL_10116.1 | 1 | Kink-turn-like Hairpin Loop |
| 250 | HL_98233.1 | 1 | |
| 251 | HL_30008.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_67042.12 | 231 | GNRA Hairpin motifs |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_27819.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_20920.1 | 1 |