Motif Atlas Releases 1.7 and 1.8
Changes in PDB files used for clustering
Release 1.7 has 213 PDB files, release 1.8 has 216 PDB files, 213 of them are identical.
No equivalence class representatives have been replaced.
3 new structures in release 1.8: 4L8H, 4MGM, 4MGN.
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 1.7 has 250 motif groups, release 1.8 has 254 motif groups, 232 of them are identical.
10 motif groups were updated, 8 groups are present only in release 1.7, 12 groups are only in release 1.8.
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_67042.9 | 226 | GNRA Hairpin motifs |
| 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_49036.3 | 12 | GNRA with one bulged base |
| 8 | HL_48039.2 | 11 | MS2 virus RNA Hairpin |
| 9 | HL_75759.3 | 10 | LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56. |
| 10 | HL_46175.2 | 10 | 16S helix 23 and 24 hairpin loops |
| 11 | HL_56824.2 | 10 | LSU Helix 60A. LSU Helix 63A. |
| 12 | HL_68081.3 | 10 | LSU Helix 20 Hairpin loop |
| 13 | HL_27271.1 | 10 | LSU Helix 96 (H96) Hairpin Loop |
| 14 | HL_17723.4 | 10 | LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot. |
| 15 | HL_80459.3 | 9 | |
| 16 | HL_87844.2 | 9 | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. |
| 17 | HL_82294.3 | 8 | SSU Helix 37 (h37) Hairpin loop. |
| 18 | HL_34027.2 | 8 | 5S Loop C - Upper part of Hairpin Loop. |
| 19 | HL_15603.1 | 8 | U1A protein-binding Hairpin Loop. |
| 20 | HL_24544.2 | 8 | LSU Helix 53 (H53) Hairpin Loop. T-loop like. |
| 21 | HL_33402.3 | 8 | LSU Helix 13 (H13) Hairpin loop. GNRA-like. |
| 22 | HL_11547.2 | 8 | LSU Helix 80 (H80) P-site Hairpin Loop. |
| 23 | HL_41833.2 | 6 | LSU Helix 81 (H81) Hairpin Loop |
| 24 | HL_70420.2 | 6 | LSU Helix 97 Hairpin loop |
| 25 | HL_75579.2 | 6 | |
| 26 | HL_87136.2 | 6 | LSU Helix 39A Hairpin loop |
| 27 | HL_01926.3 | 6 | LSU Helix 71 (H71) Hairpin Loop. |
| 28 | HL_34108.2 | 6 | LSU Helix 37 (H37) Hairpin Loop. |
| 29 | HL_46489.2 | 6 | LSU H89 Hairpin Loop |
| 30 | HL_39872.2 | 6 | LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA. |
| 31 | HL_57514.2 | 6 | Two base, cross-stacked hairpin loop |
| 32 | HL_11509.2 | 6 | LSU Helix 6 (H6) Hairpin Loop. |
| 33 | HL_39942.2 | 6 | LSU Helix 91 (H91) Hairpin Loop |
| 34 | HL_18156.2 | 6 | LSU Helix 72 (H72) Hairpin Loop |
| 35 | HL_62228.3 | 5 | LSU Helix 35A (H35A) Hairpin Loop |
| 36 | HL_45018.3 | 5 | Hairpin-Hairpin Interacting HL |
| 37 | HL_78731.1 | 5 | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot |
| 38 | HL_72273.1 | 5 | tRNA D-loop |
| 39 | HL_66174.1 | 5 | cHS GU/cWS Double Platform creates Intercalation site |
| 40 | HL_72543.2 | 5 | LSU Helix 43 (H43) Hairpin Loop. T-loop Like. |
| 41 | HL_95720.1 | 5 | Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 42 | HL_88311.2 | 5 | LSU Helix 35 (H35) Hairpin Loop |
| 43 | HL_85534.1 | 5 | LSU Helix 65 (H65) Hairpin Loop. T-loop like. |
| 44 | HL_06643.2 | 5 | tRNA D-loop. Sec tRNA |
| 45 | HL_55718.1 | 4 | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56. |
| 46 | HL_29831.1 | 4 | GNRA-like with bulged base. |
| 47 | HL_48116.2 | 4 | GNRA-like with 5'-stacking of first unpaired base. |
| 48 | HL_62881.1 | 4 | RNase P Structured Hairpin Loop |
| 49 | HL_98523.2 | 4 | GNRA-like. Closed by tSH UC. |
| 50 | HL_11376.1 | 4 | LSU Helix 8 (H8) Hairpin Loop |
| 51 | HL_47784.2 | 4 | SSU Central Pseudoknot (forms helix 2) |
| 52 | HL_64543.2 | 4 | SSU Helix 31 (h31) Hairpin Loop |
| 53 | HL_23971.1 | 4 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 54 | HL_33875.1 | 3 | SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like. |
| 55 | HL_41827.1 | 3 | |
| 56 | HL_74686.1 | 3 | SSU Central Pseudoknot (forms helix 2) |
| 57 | HL_13707.2 | 3 | cSH AA Platform containing Hairpin Loop |
| 58 | HL_19905.3 | 3 | LSU: Part of IL/3WJ between H55 and H56. |
| 59 | HL_08382.2 | 3 | |
| 60 | HL_42077.2 | 3 | LSU Helix 28 (H28) Hairpin Loop |
| 61 | HL_48254.1 | 3 | LSU Helix 84 (H84) Hairpin Loop. |
| 62 | HL_19221.2 | 3 | |
| 63 | HL_76036.3 | 3 | LSU Helix 8 (H8) Hairpin Loop |
| 64 | HL_23182.1 | 3 | |
| 65 | HL_80492.2 | 3 | tRNA D-loop |
| 66 | HL_25124.1 | 3 | tSW GA closed tetraloops |
| 67 | HL_27429.3 | 3 | |
| 68 | HL_68697.2 | 3 | |
| 69 | HL_58083.2 | 3 | |
| 70 | HL_61547.4 | 3 | |
| 71 | HL_78361.1 | 3 | |
| 72 | HL_38130.2 | 2 | |
| 73 | HL_50312.1 | 2 | |
| 74 | HL_86398.1 | 2 | |
| 75 | HL_90542.1 | 2 | |
| 76 | HL_94578.1 | 2 | |
| 77 | HL_18587.1 | 2 | |
| 78 | HL_65347.1 | 2 | SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops |
| 79 | HL_24473.3 | 2 | tRNA D-loop |
| 80 | HL_26495.1 | 2 | |
| 81 | HL_91693.1 | 2 | |
| 82 | HL_21545.1 | 2 | LSU Helix 96 (H96) Hairpin Loop |
| 83 | HL_62967.1 | 2 | |
| 84 | HL_65924.1 | 2 | |
| 85 | HL_84353.1 | 2 | |
| 86 | HL_87554.1 | 2 | |
| 87 | HL_91872.1 | 2 | |
| 88 | HL_03791.1 | 2 | |
| 89 | HL_16770.1 | 2 | |
| 90 | HL_23129.1 | 2 | |
| 91 | HL_42436.1 | 2 | Kissing Hairpin from di-GMP-II riboswitch |
| 92 | HL_98577.1 | 2 | |
| 93 | HL_24711.1 | 2 | |
| 94 | HL_42553.1 | 2 | |
| 95 | HL_49210.1 | 2 | |
| 96 | HL_54751.2 | 2 | |
| 97 | HL_60200.1 | 2 | |
| 98 | HL_96915.1 | 2 | |
| 99 | HL_05361.1 | 2 | |
| 100 | HL_19399.1 | 2 | |
| 101 | HL_64371.2 | 2 | |
| 102 | HL_99633.1 | 2 | |
| 103 | HL_06122.1 | 2 | |
| 104 | HL_17790.1 | 2 | UNCG-like. cWW Closing pair. |
| 105 | HL_23290.1 | 2 | |
| 106 | HL_33451.1 | 2 | |
| 107 | HL_66948.1 | 2 | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base |
| 108 | HL_74559.1 | 2 | Two base, cross-stacked hairpin loop |
| 109 | HL_86123.2 | 2 | SSU Helix 42 (h42) Hairpin Loop. T-loop like. |
| 110 | HL_93771.1 | 2 | tRNA T-loop distorted by RS binding |
| 111 | HL_19528.1 | 2 | |
| 112 | HL_44522.1 | 1 | |
| 113 | HL_58223.1 | 1 | |
| 114 | HL_65071.1 | 1 | |
| 115 | HL_67000.1 | 1 | |
| 116 | HL_69403.1 | 1 | GNRA-like |
| 117 | HL_78420.1 | 1 | |
| 118 | HL_97499.1 | 1 | |
| 119 | HL_01418.1 | 1 | |
| 120 | HL_07915.1 | 1 | |
| 121 | HL_24108.1 | 1 | |
| 122 | HL_25197.1 | 1 | |
| 123 | HL_38138.1 | 1 | |
| 124 | HL_52540.1 | 1 | |
| 125 | HL_56775.1 | 1 | |
| 126 | HL_58601.1 | 1 | |
| 127 | HL_62880.1 | 1 | |
| 128 | HL_78507.1 | 1 | |
| 129 | HL_83865.1 | 1 | |
| 130 | HL_94697.1 | 1 | LSU Helix 84 (H84) Hairpin Loop. E.coli. |
| 131 | HL_97784.1 | 1 | |
| 132 | HL_13786.1 | 1 | |
| 133 | HL_20806.1 | 1 | |
| 134 | HL_30008.1 | 1 | |
| 135 | HL_38897.1 | 1 | S8 operon binding Hairpin Loop. T-loop like with purine stacking. |
| 136 | HL_45411.1 | 1 | |
| 137 | HL_56809.1 | 1 | |
| 138 | HL_59182.1 | 1 | |
| 139 | HL_65802.1 | 1 | |
| 140 | HL_67761.1 | 1 | |
| 141 | HL_70912.1 | 1 | |
| 142 | HL_84289.1 | 1 | |
| 143 | HL_87223.1 | 1 | |
| 144 | HL_95049.1 | 1 | Two base, cross-stacked hairpin loop |
| 145 | HL_97971.1 | 1 | |
| 146 | HL_03785.1 | 1 | LSU Helix 8 (H8) Hairpin Loop |
| 147 | HL_10116.1 | 1 | Kink-turn-like Hairpin Loop |
| 148 | HL_19132.1 | 1 | |
| 149 | HL_26579.1 | 1 | |
| 150 | HL_30128.1 | 1 | |
| 151 | HL_34440.1 | 1 | |
| 152 | HL_39422.1 | 1 | |
| 153 | HL_42345.1 | 1 | |
| 154 | HL_48480.1 | 1 | |
| 155 | HL_53015.1 | 1 | |
| 156 | HL_59604.1 | 1 | |
| 157 | HL_75850.1 | 1 | |
| 158 | HL_79902.1 | 1 | |
| 159 | HL_95716.1 | 1 | |
| 160 | HL_10378.1 | 1 | Double 5'-stacked purine Hairpin Loop from Eukaryal LSU |
| 161 | HL_24707.1 | 1 | |
| 162 | HL_30366.1 | 1 | LSU Helix 10 (H10) Hairpin E.coli |
| 163 | HL_35200.1 | 1 | |
| 164 | HL_39486.1 | 1 | |
| 165 | HL_53789.1 | 1 | |
| 166 | HL_57217.1 | 1 | cHS platform Intercalation Site |
| 167 | HL_59610.1 | 1 | |
| 168 | HL_62970.1 | 1 | |
| 169 | HL_68435.1 | 1 | |
| 170 | HL_84888.1 | 1 | T-loop like but without tWH UA |
| 171 | HL_93530.1 | 1 | |
| 172 | HL_04194.1 | 1 | |
| 173 | HL_17537.1 | 1 | |
| 174 | HL_19226.1 | 1 | |
| 175 | HL_27397.1 | 1 | |
| 176 | HL_33277.1 | 1 | |
| 177 | HL_35865.1 | 1 | |
| 178 | HL_46570.1 | 1 | |
| 179 | HL_63304.1 | 1 | |
| 180 | HL_66467.1 | 1 | |
| 181 | HL_68579.1 | 1 | |
| 182 | HL_73465.1 | 1 | |
| 183 | HL_77692.1 | 1 | tRNA D-loop |
| 184 | HL_85018.1 | 1 | |
| 185 | HL_93567.1 | 1 | |
| 186 | HL_99207.1 | 1 | Tetrahymena LSU hairpin poorly modeled |
| 187 | HL_23195.1 | 1 | |
| 188 | HL_36842.1 | 1 | |
| 189 | HL_42969.1 | 1 | |
| 190 | HL_47337.1 | 1 | |
| 191 | HL_49492.1 | 1 | Forms 7-BP PseudoKnot. Has embedded sarcin-like motif |
| 192 | HL_55202.1 | 1 | U2B"-U2A" binding hairpin loop |
| 193 | HL_57843.1 | 1 | |
| 194 | HL_60203.1 | 1 | |
| 195 | HL_66877.1 | 1 | cSH GU/cWS double platform, intercalation site |
| 196 | HL_73972.1 | 1 | |
| 197 | HL_78228.1 | 1 | |
| 198 | HL_82243.1 | 1 | |
| 199 | HL_88960.1 | 1 | |
| 200 | HL_93633.1 | 1 | |
| 201 | HL_96994.1 | 1 | |
| 202 | HL_19452.1 | 1 | tRNA D-loop |
| 203 | HL_25175.1 | 1 | |
| 204 | HL_27819.1 | 1 | |
| 205 | HL_37962.1 | 1 | |
| 206 | HL_44390.1 | 1 | |
| 207 | HL_50059.1 | 1 | LSU Helix 35 (H35) Hairpin Loop from Yeast |
| 208 | HL_55272.1 | 1 | |
| 209 | HL_68733.1 | 1 | LSU Yeast Hairpin Loop |
| 210 | HL_82288.1 | 1 | |
| 211 | HL_90102.1 | 1 | Kink-turn-like Hairpin Loop |
| 212 | HL_00090.1 | 1 | |
| 213 | HL_12706.1 | 1 | |
| 214 | HL_25195.1 | 1 | |
| 215 | HL_29196.1 | 1 | |
| 216 | HL_33640.1 | 1 |
Updated motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_72498.10 | 66 | T-loops with two bulged bases |
| 2 | HL_74465.3 | 13 | tRNA Anti-Codon loop |
| 3 | HL_42677.2 | 7 | |
| 4 | HL_06997.2 | 3 | |
| 5 | HL_90579.3 | 3 | LSU Helix 69 (H69) Hairpin Loop |
| 6 | HL_21675.2 | 3 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 7 | HL_98833.3 | 3 | |
| 8 | HL_42687.4 | 3 | |
| 9 | HL_76766.3 | 2 | |
| 10 | HL_32644.2 | 2 | LSU Helix 69 (H69) Hairpin Loop |
Removed motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_12595.2 | 3 | |
| 2 | HL_75575.1 | 2 | |
| 3 | HL_81752.1 | 2 | |
| 4 | HL_06312.1 | 2 | |
| 5 | HL_26143.1 | 2 | |
| 6 | HL_53753.1 | 2 | |
| 7 | HL_07315.1 | 1 | |
| 8 | HL_71607.1 | 1 |
Added motif groups
| # | Motif id | Instances | Description |
|---|---|---|---|
| 1 | HL_35619.1 | 3 | |
| 2 | HL_65249.1 | 2 | |
| 3 | HL_74505.1 | 2 | |
| 4 | HL_42094.1 | 2 | |
| 5 | HL_63941.1 | 2 | |
| 6 | HL_28676.1 | 1 | |
| 7 | HL_76585.1 | 1 | |
| 8 | HL_76679.1 | 1 | |
| 9 | HL_84768.1 | 1 | |
| 10 | HL_52116.1 | 1 | |
| 11 | HL_98234.1 | 1 | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking |
| 12 | HL_59225.1 | 1 |