Motif Atlas Releases 0.5 and 0.6
Changes in PDB files used for clustering
Release 0.5 has 206 PDB files, release 0.6 has 207 PDB files, 203 of them are identical.
3 equivalence classes changed representatives: 3U4M → 3UMY, 3G78 → 4FAW, 2FK6 → 4GCW.
1 new structures in release 0.6: 4FY3.
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 0.5 has 247 motif groups, release 0.6 has 245 motif groups, 227 of them are identical.
4 motif groups were updated, 16 groups are present only in release 0.5, 14 groups are only in release 0.6.
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_18781.1 | 21 | Double sheared (tSH) with U-turn |
| 2 | HL_91226.2 | 17 | Kissing Hairpin motif |
| 3 | HL_97270.1 | 15 | T-loops with 1 bulged base |
| 4 | HL_52574.1 | 15 | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. |
| 5 | HL_80459.1 | 11 | |
| 6 | HL_48039.1 | 11 | MS2 virus RNA Hairpin |
| 7 | HL_74465.1 | 11 | tRNA Anti-Codon loop |
| 8 | HL_68081.2 | 10 | LSU Helix 20 Hairpin loop |
| 9 | HL_75759.1 | 10 | LSU: Part of IL/3WJ between H55 and H56. |
| 10 | HL_49036.1 | 10 | GNRA with one bulged base |
| 11 | HL_56824.1 | 10 | LSU Helix 60A. LSU Helix 63A. |
| 12 | HL_46175.1 | 10 | 16S helix 23 and 24 hairpin loops |
| 13 | HL_17723.1 | 9 | LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot. |
| 14 | HL_87844.1 | 9 | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. |
| 15 | HL_28436.2 | 9 | LSU Helix 96 (H96) Hairpin Loop |
| 16 | HL_15603.1 | 8 | U1A protein-binding Hairpin Loop. |
| 17 | HL_11547.1 | 8 | LSU Helix 80 (H80) P-site Hairpin Loop. |
| 18 | HL_82294.2 | 8 | SSU Helix 37 (h37) Hairpin loop. |
| 19 | HL_24544.1 | 8 | LSU Helix 53 (H53) Hairpin Loop. T-loop like. |
| 20 | HL_33402.1 | 7 | LSU Helix 13 (H13) Hairpin loop. GNRA-like. |
| 21 | HL_01926.1 | 7 | LSU Helix 71 (H71) Hairpin Loop. |
| 22 | HL_34027.1 | 7 | 5S Loop C - Upper part of Hairpin Loop. |
| 23 | HL_70420.1 | 6 | LSU Helix 97 Hairpin loop |
| 24 | HL_34108.1 | 6 | LSU Helix 37 (H37) Hairpin Loop. |
| 25 | HL_18156.1 | 6 | LSU Helix 72 (H72) Hairpin Loop |
| 26 | HL_39872.1 | 6 | LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA. |
| 27 | HL_75579.1 | 6 | |
| 28 | HL_87136.1 | 6 | LSU Helix 39A Hairpin loop |
| 29 | HL_11509.1 | 6 | LSU Helix 6 (H6) Hairpin Loop. |
| 30 | HL_41833.1 | 6 | LSU Helix 81 (H81) Hairpin Loop |
| 31 | HL_42677.1 | 6 | |
| 32 | HL_46489.1 | 6 | LSU H89 Hairpin Loop |
| 33 | HL_39942.1 | 6 | LSU Helix 91 (H91) Hairpin Loop |
| 34 | HL_19261.1 | 5 | SSU Central Pseudoknot (forms helix 2) |
| 35 | HL_06643.1 | 5 | tRNA D-loop. Sec tRNA |
| 36 | HL_12811.1 | 5 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 37 | HL_78731.1 | 5 | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot |
| 38 | HL_72543.1 | 5 | LSU Helix 43 (H43) Hairpin Loop. T-loop Like. |
| 39 | HL_72273.1 | 5 | tRNA D-loop |
| 40 | HL_88311.1 | 5 | LSU Helix 35 (H35) Hairpin Loop |
| 41 | HL_85534.1 | 5 | LSU Helix 65 (H65) Hairpin Loop. T-loop like. |
| 42 | HL_66174.1 | 5 | cHS GU/cWS Double Platform creates Intercalation site |
| 43 | HL_95423.1 | 4 | UNCG-like. cWW Closing pair. |
| 44 | HL_62228.1 | 4 | LSU Helix 35A (H35A) Hairpin Loop |
| 45 | HL_64543.1 | 4 | SSU Helix 31 (h31) Hairpin Loop |
| 46 | HL_62881.1 | 4 | RNase P Structured Hairpin Loop |
| 47 | HL_48116.1 | 4 | GNRA-like with 5'-stacking of first unpaired base. |
| 48 | HL_08382.1 | 4 | |
| 49 | HL_98523.1 | 4 | GNRA-like. Closed by tSH UC. |
| 50 | HL_29831.1 | 4 | GNRA-like with bulged base. |
| 51 | HL_45018.2 | 4 | |
| 52 | HL_53664.1 | 3 | Double tSH (double sheared) with bulged base |
| 53 | HL_19221.2 | 3 | |
| 54 | HL_32644.1 | 3 | LSU Helix 69 (H69) Hairpin Loop |
| 55 | HL_13707.2 | 3 | cSH AA Platform containing Hairpin Loop |
| 56 | HL_48254.1 | 3 | LSU Helix 84 (H84) Hairpin Loop. |
| 57 | HL_54751.1 | 3 | |
| 58 | HL_42687.2 | 3 | |
| 59 | HL_58083.2 | 3 | |
| 60 | HL_82253.1 | 3 | |
| 61 | HL_64371.1 | 3 | |
| 62 | HL_73023.1 | 3 | Two base, cross-stacked hairpin loop |
| 63 | HL_98833.1 | 3 | |
| 64 | HL_90579.1 | 3 | |
| 65 | HL_41827.1 | 3 | |
| 66 | HL_42077.2 | 3 | LSU Helix 28 (H28) Hairpin Loop |
| 67 | HL_23182.1 | 3 | |
| 68 | HL_76036.1 | 3 | LSU Helix 8 (H8) Hairpin Loop |
| 69 | HL_25124.1 | 3 | tSW GA closed tetraloops |
| 70 | HL_20739.1 | 3 | |
| 71 | HL_46794.2 | 3 | |
| 72 | HL_80492.2 | 3 | tRNA D-loop |
| 73 | HL_27429.2 | 3 | |
| 74 | HL_78361.1 | 3 | |
| 75 | HL_06122.1 | 2 | |
| 76 | HL_24473.3 | 2 | tRNA D-loop |
| 77 | HL_46981.1 | 2 | |
| 78 | HL_88640.1 | 2 | |
| 79 | HL_19399.1 | 2 | |
| 80 | HL_67692.1 | 2 | |
| 81 | HL_26057.1 | 2 | |
| 82 | HL_16770.1 | 2 | |
| 83 | HL_57904.1 | 2 | |
| 84 | HL_70106.1 | 2 | LSU Helix 10 (H10) Hairpin E.coli |
| 85 | HL_87554.1 | 2 | |
| 86 | HL_05361.1 | 2 | |
| 87 | HL_49267.1 | 2 | |
| 88 | HL_98577.1 | 2 | |
| 89 | HL_70459.1 | 2 | |
| 90 | HL_99633.1 | 2 | |
| 91 | HL_96915.1 | 2 | |
| 92 | HL_38130.2 | 2 | |
| 93 | HL_42436.1 | 2 | Kissing Hairpin from di-GMP-II riboswitch |
| 94 | HL_03791.1 | 2 | |
| 95 | HL_65924.1 | 2 | |
| 96 | HL_86123.2 | 2 | SSU Helix 42 (h42) Hairpin Loop. T-loop like. |
| 97 | HL_42553.1 | 2 | |
| 98 | HL_57014.1 | 2 | |
| 99 | HL_05510.1 | 2 | |
| 100 | HL_44467.1 | 2 | |
| 101 | HL_49210.1 | 2 | |
| 102 | HL_19905.1 | 2 | |
| 103 | HL_81555.1 | 2 | |
| 104 | HL_05797.1 | 2 | |
| 105 | HL_63823.1 | 2 | |
| 106 | HL_24711.1 | 2 | |
| 107 | HL_23290.1 | 2 | |
| 108 | HL_94578.1 | 2 | |
| 109 | HL_33451.1 | 2 | |
| 110 | HL_14013.1 | 2 | |
| 111 | HL_76105.1 | 2 | |
| 112 | HL_76766.1 | 2 | |
| 113 | HL_59610.1 | 1 | |
| 114 | HL_55543.1 | 1 | |
| 115 | HL_93567.1 | 1 | |
| 116 | HL_15771.1 | 1 | |
| 117 | HL_42969.1 | 1 | |
| 118 | HL_57843.1 | 1 | |
| 119 | HL_68579.1 | 1 | |
| 120 | HL_70912.1 | 1 | |
| 121 | HL_13786.1 | 1 | |
| 122 | HL_04194.1 | 1 | |
| 123 | HL_75850.1 | 1 | |
| 124 | HL_39486.1 | 1 | |
| 125 | HL_97784.1 | 1 | |
| 126 | HL_94145.1 | 1 | SSU Helix 43 (h43) Hairpin Loop E.coli |
| 127 | HL_45411.1 | 1 | |
| 128 | HL_99779.1 | 1 | |
| 129 | HL_78507.1 | 1 | |
| 130 | HL_87223.1 | 1 | |
| 131 | HL_00721.1 | 1 | |
| 132 | HL_63411.1 | 1 | |
| 133 | HL_45358.1 | 1 | Double hairpin loop based on GGA triple |
| 134 | HL_84888.1 | 1 | T-loop like but without tWH UA |
| 135 | HL_19132.1 | 1 | |
| 136 | HL_91613.1 | 1 | |
| 137 | HL_62970.1 | 1 | |
| 138 | HL_50059.1 | 1 | LSU Helix 35 (H35) Hairpin Loop from Yeast |
| 139 | HL_33277.1 | 1 | |
| 140 | HL_66900.1 | 1 | |
| 141 | HL_55202.1 | 1 | U2B"-U2A" binding hairpin loop |
| 142 | HL_38897.1 | 1 | S8 operon binding Hairpin Loop. T-loop like with purine stacking. |
| 143 | HL_07315.1 | 1 | |
| 144 | HL_94697.1 | 1 | LSU Helix 84 (H84) Hairpin Loop. E.coli. |
| 145 | HL_63690.1 | 1 | |
| 146 | HL_65071.1 | 1 | |
| 147 | HL_68435.1 | 1 | |
| 148 | HL_88960.1 | 1 | |
| 149 | HL_85753.1 | 1 | |
| 150 | HL_62880.1 | 1 | |
| 151 | HL_66467.1 | 1 | |
| 152 | HL_10116.1 | 1 | Kink-turn-like Hairpin Loop |
| 153 | HL_24707.1 | 1 | |
| 154 | HL_53789.1 | 1 | |
| 155 | HL_25195.1 | 1 | |
| 156 | HL_02479.1 | 1 | |
| 157 | HL_61061.1 | 1 | |
| 158 | HL_58223.1 | 1 | |
| 159 | HL_58601.1 | 1 | |
| 160 | HL_66877.1 | 1 | cSH GU/cWS double platform, intercalation site |
| 161 | HL_67000.1 | 1 | |
| 162 | HL_96192.1 | 1 | |
| 163 | HL_47337.1 | 1 | |
| 164 | HL_68733.1 | 1 | LSU Yeast Hairpin Loop |
| 165 | HL_82243.1 | 1 | |
| 166 | HL_85018.1 | 1 | |
| 167 | HL_38898.1 | 1 | |
| 168 | HL_38138.1 | 1 | |
| 169 | HL_33640.1 | 1 | |
| 170 | HL_65802.1 | 1 | |
| 171 | HL_35865.1 | 1 | |
| 172 | HL_25197.1 | 1 | |
| 173 | HL_58786.1 | 1 | |
| 174 | HL_97499.1 | 1 | |
| 175 | HL_35004.1 | 1 | |
| 176 | HL_03431.1 | 1 | |
| 177 | HL_00238.1 | 1 | |
| 178 | HL_26579.1 | 1 | |
| 179 | HL_66880.1 | 1 | |
| 180 | HL_44390.1 | 1 | |
| 181 | HL_10378.1 | 1 | Double 5'-stacked purine Hairpin Loop from Eukaryal LSU |
| 182 | HL_78420.1 | 1 | |
| 183 | HL_90102.1 | 1 | Kink-turn-like Hairpin Loop |
| 184 | HL_69403.1 | 1 | GNRA-like |
| 185 | HL_98233.1 | 1 | |
| 186 | HL_17008.1 | 1 | Nova-2 KH3 domain binding hairpin |
| 187 | HL_23522.1 | 1 | |
| 188 | HL_27831.1 | 1 | |
| 189 | HL_59604.1 | 1 | |
| 190 | HL_37962.1 | 1 | |
| 191 | HL_93206.1 | 1 | |
| 192 | HL_44522.1 | 1 | |
| 193 | HL_84289.1 | 1 | |
| 194 | HL_27397.1 | 1 | |
| 195 | HL_56809.1 | 1 | |
| 196 | HL_63304.1 | 1 | |
| 197 | HL_25175.1 | 1 | |
| 198 | HL_95716.1 | 1 | |
| 199 | HL_82288.1 | 1 | |
| 200 | HL_83053.1 | 1 | SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like. |
| 201 | HL_56775.1 | 1 | |
| 202 | HL_48480.1 | 1 | |
| 203 | HL_57217.1 | 1 | cHS platform Intercalation Site |
| 204 | HL_81780.1 | 1 | |
| 205 | HL_90365.1 | 1 | 5S rRNA Loop C from D.radiodurans |
| 206 | HL_39422.1 | 1 | |
| 207 | HL_34440.1 | 1 | |
| 208 | HL_27819.1 | 1 | |
| 209 | HL_00090.1 | 1 | |
| 210 | HL_55272.1 | 1 | |
| 211 | HL_97971.1 | 1 | |
| 212 | HL_36842.1 | 1 | |
| 213 | HL_33524.1 | 1 | tRNA T-loop distorted by RS binding |
| 214 | HL_81661.1 | 1 | tRNA D-loop |
| 215 | HL_17468.1 | 1 | |
| 216 | HL_30128.1 | 1 | |
| 217 | HL_20806.1 | 1 | |
| 218 | HL_20914.1 | 1 | |
| 219 | HL_05113.1 | 1 | |
| 220 | HL_79902.1 | 1 | |
| 221 | HL_30731.1 | 1 | |
| 222 | HL_12706.1 | 1 | |
| 223 | HL_67761.1 | 1 | |
| 224 | HL_53015.1 | 1 | |
| 225 | HL_78228.1 | 1 | |
| 226 | HL_35200.1 | 1 | |
| 227 | HL_99207.1 | 1 | Tetrahymena LSU hairpin poorly modeled |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_67042.3 | 222 | GNRA Hairpin motifs |
| 2 | HL_72498.4 | 62 | T-loops with two bulged bases |
| 3 | HL_39895.3 | 34 | UNCG Hairpin motifs |
| 4 | HL_61547.2 | 3 |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_27658.1 | 3 | |
| 2 | HL_63668.1 | 2 | |
| 3 | HL_20857.1 | 2 | |
| 4 | HL_27809.1 | 2 | |
| 5 | HL_94243.1 | 2 | |
| 6 | HL_10832.1 | 2 | |
| 7 | HL_56859.1 | 2 | |
| 8 | HL_10842.1 | 1 | |
| 9 | HL_60420.1 | 1 | |
| 10 | HL_20252.1 | 1 | |
| 11 | HL_76027.1 | 1 | |
| 12 | HL_77981.1 | 1 | |
| 13 | HL_79390.1 | 1 | |
| 14 | HL_35446.1 | 1 | |
| 15 | HL_88921.1 | 1 | |
| 16 | HL_39922.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_06312.1 | 2 | |
| 2 | HL_75575.1 | 2 | |
| 3 | HL_12595.1 | 2 | |
| 4 | HL_77555.1 | 2 | |
| 5 | HL_81752.1 | 2 | |
| 6 | HL_84353.1 | 2 | |
| 7 | HL_93015.1 | 2 | |
| 8 | HL_53753.1 | 2 | |
| 9 | HL_68697.1 | 2 | |
| 10 | HL_17537.1 | 1 | |
| 11 | HL_19452.1 | 1 | tRNA D-loop |
| 12 | HL_49492.1 | 1 | Forms 7-BP PseudoKnot. Has embedded sarcin-like motif |
| 13 | HL_01987.1 | 1 | |
| 14 | HL_71607.1 | 1 |