Motif Atlas Releases 1.8 and 1.9
Changes in PDB files used for clustering
Release 1.8 has 205 PDB files, release 1.9 has 209 PDB files, 205 of them are identical.
No equivalence class representatives have been replaced.
4 new structures in release 1.9: 4BW0, 4C7O, 4K27, 4LGT.
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 1.8 has 272 motif groups, release 1.9 has 271 motif groups, 251 of them are identical.
14 motif groups were updated, 7 groups are present only in release 1.8, 6 groups are only in release 1.9.
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_47174.8 | 205 | cWW AG or water inserted cWW Y-Y. |
2 | IL_39199.4 | 53 | Hoogsteen-edge Platform, Single bulged base |
3 | IL_56465.3 | 46 | Single, unpaired intercalated base, consensus A |
4 | IL_44540.4 | 43 | Sugar-edge, 1-base platform, consensus tHS |
5 | IL_87904.5 | 31 | Triple sheared (tSH-tHS-tHS) no inserted bases |
6 | IL_82444.1 | 29 | cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif |
7 | IL_13959.4 | 26 | Double Sheared (tSH-tHS) |
8 | IL_73276.5 | 22 | C-loop |
9 | IL_65553.7 | 22 | Kink-turn |
10 | IL_93424.4 | 21 | tSH-inserted-tHW |
11 | IL_55938.4 | 18 | LSU Helix 89 (H89) IL2. cSH Platform. |
12 | IL_92027.3 | 17 | 16S h21 S8 binding site |
13 | IL_85647.3 | 16 | Sarcin-ricin parent motif with 15 Nts |
14 | IL_24982.5 | 16 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
15 | IL_94430.5 | 16 | 16S h32-h33-h34 3WJ |
16 | IL_92109.2 | 15 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
17 | IL_31555.4 | 13 | Tandem sheared with inserted, unpaired purine. |
18 | IL_49493.4 | 13 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
19 | IL_37104.2 | 11 | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
20 | IL_43124.2 | 11 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
21 | IL_17212.1 | 10 | cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif |
22 | IL_24546.4 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
23 | IL_58291.4 | 10 | Recurrent Sub-motif found in junctions |
24 | IL_47444.3 | 9 | SRP Loop E-like motif |
25 | IL_90459.3 | 9 | cWW AG or UU |
26 | IL_92114.3 | 9 | GAAA loop receptor "platform" motif |
27 | IL_02809.3 | 9 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
28 | IL_92321.4 | 7 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
29 | IL_73000.2 | 7 | cHS-cWS |
30 | IL_83451.3 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
31 | IL_25380.1 | 6 | LSU Helix 89 (H89) IL2 |
32 | IL_53635.3 | 6 | LSU Helix 32 (H32) IL |
33 | IL_90133.3 | 6 | |
34 | IL_13069.3 | 6 | LSU 3WJ H32-H33-H35A |
35 | IL_72158.3 | 6 | LSU Helix 62 (H62) IL |
36 | IL_97057.3 | 6 | |
37 | IL_77263.2 | 6 | Kink-turn from U4 |
38 | IL_25230.3 | 6 | Bacterial 5S rRNA Loop E |
39 | IL_39585.1 | 6 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
40 | IL_08926.3 | 6 | 23S H91 IL |
41 | IL_70237.3 | 6 | |
42 | IL_02359.3 | 5 | |
43 | IL_44067.4 | 5 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
44 | IL_05684.1 | 5 | tHS tHH bulge with S-turn | Double S-turn motif |
45 | IL_86357.3 | 5 | LSU Helix 61 IL2 |
46 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
47 | IL_79083.3 | 5 | |
48 | IL_01080.1 | 4 | |
49 | IL_34363.2 | 4 | Kink-turn from 23S H42 |
50 | IL_38807.3 | 4 | |
51 | IL_95652.3 | 4 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
52 | IL_09530.1 | 4 | Double S-turn motif |
53 | IL_21333.2 | 4 | tSH-tHW-bulge |
54 | IL_31066.3 | 4 | SSU Helix 44 (h44) extension |
55 | IL_98591.3 | 4 | |
56 | IL_28572.2 | 4 | 16S h18 kink-turn like motif |
57 | IL_45262.4 | 4 | |
58 | IL_15709.1 | 4 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
59 | IL_31663.1 | 4 | 23S H73 ILa : Part of larger Motif |
60 | IL_39526.4 | 4 | |
61 | IL_47758.2 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
62 | IL_93568.2 | 4 | Triple Sheared (tSH-tHS-tHS) with wobble cWW. |
63 | IL_22732.1 | 4 | tSH-inserted-tHS |
64 | IL_42251.1 | 4 | |
65 | IL_39980.1 | 4 | |
66 | IL_82188.2 | 4 | LSU H68 IL from H.m. |
67 | IL_16415.2 | 3 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
68 | IL_30840.2 | 3 | |
69 | IL_43946.1 | 3 | |
70 | IL_75447.1 | 3 | |
71 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
72 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
73 | IL_34628.2 | 3 | Kink-turn |
74 | IL_35043.1 | 3 | cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base |
75 | IL_52173.1 | 3 | |
76 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
77 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
78 | IL_62499.7 | 3 | |
79 | IL_05723.1 | 3 | |
80 | IL_07300.2 | 3 | |
81 | IL_89028.6 | 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. |
82 | IL_06180.1 | 3 | tHS tHH bulge with S-turn |
83 | IL_16166.4 | 3 | 23S H91 IL |
84 | IL_25271.2 | 3 | SSU Helix 8 (h8) IL E.c. and Yeast |
85 | IL_58586.2 | 3 | |
86 | IL_74876.2 | 3 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
87 | IL_87065.1 | 3 | 23S H91 IL | Single-Base Intercalation Site |
88 | IL_98421.4 | 3 | SSU Helix 12 (h12) IL |
89 | IL_50521.1 | 2 | |
90 | IL_98566.1 | 2 | |
91 | IL_40892.1 | 2 | |
92 | IL_67887.1 | 2 | |
93 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
94 | IL_80093.1 | 2 | |
95 | IL_87548.1 | 2 | |
96 | IL_09587.1 | 2 | |
97 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
98 | IL_90735.1 | 2 | |
99 | IL_09882.1 | 2 | |
100 | IL_21495.1 | 2 | |
101 | IL_39355.1 | 2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1 |
102 | IL_68880.1 | 2 | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
103 | IL_77076.1 | 2 | |
104 | IL_21639.1 | 2 | |
105 | IL_45794.1 | 2 | |
106 | IL_69536.1 | 2 | LSU Helix 96 (H96) IL2 |
107 | IL_97509.1 | 2 | Double sheared with wobble cWW. |
108 | IL_11751.1 | 2 | |
109 | IL_15840.2 | 2 | Triple Sheared with unpaired, inserted A |
110 | IL_19898.1 | 2 | |
111 | IL_31707.1 | 2 | Vitamin B12 aptamer |
112 | IL_37197.1 | 2 | |
113 | IL_52940.1 | 2 | |
114 | IL_74214.1 | 2 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
115 | IL_97833.1 | 2 | |
116 | IL_23262.4 | 2 | |
117 | IL_46435.1 | 2 | |
118 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
119 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
120 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
121 | IL_00998.1 | 2 | |
122 | IL_12211.1 | 2 | |
123 | IL_16330.1 | 2 | |
124 | IL_23414.1 | 2 | |
125 | IL_30381.1 | 2 | tHS tHH bulge with S-turn |
126 | IL_33964.1 | 2 | |
127 | IL_37406.1 | 2 | |
128 | IL_85015.1 | 2 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
129 | IL_87507.1 | 2 | tHS tHH bulge with S-turn |
130 | IL_90057.1 | 2 | |
131 | IL_03741.1 | 1 | |
132 | IL_06421.1 | 1 | Single sheared with bulged bases |
133 | IL_09491.1 | 1 | |
134 | IL_12507.1 | 1 | |
135 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
136 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
137 | IL_40845.1 | 1 | |
138 | IL_56513.1 | 1 | |
139 | IL_59934.1 | 1 | SSU Helix 23 (h23) Kink-turn E. coli |
140 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
141 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
142 | IL_85510.1 | 1 | |
143 | IL_87523.1 | 1 | |
144 | IL_05221.1 | 1 | |
145 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
146 | IL_26868.1 | 1 | |
147 | IL_50911.1 | 1 | 16S h34 ILa : Part of larger motif |
148 | IL_53988.1 | 1 | |
149 | IL_57364.1 | 1 | LSU Helix 89 (H89) IL2 |
150 | IL_60649.1 | 1 | Kink-turn |
151 | IL_71942.1 | 1 | |
152 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |
153 | IL_95980.1 | 1 | 23S H73 ILa : Part of larger Motif | Single sheared with bulged bases |
154 | IL_05513.1 | 1 | |
155 | IL_06471.1 | 1 | |
156 | IL_17603.1 | 1 | |
157 | IL_21421.1 | 1 | |
158 | IL_26971.1 | 1 | |
159 | IL_31224.1 | 1 | 23S H91 IL |
160 | IL_39324.1 | 1 | |
161 | IL_41139.1 | 1 | |
162 | IL_47687.1 | 1 | |
163 | IL_54450.1 | 1 | |
164 | IL_61730.1 | 1 | |
165 | IL_68767.1 | 1 | |
166 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
167 | IL_82650.1 | 1 | |
168 | IL_85805.1 | 1 | |
169 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
170 | IL_02835.1 | 1 | |
171 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
172 | IL_15205.1 | 1 | |
173 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
174 | IL_25082.1 | 1 | |
175 | IL_41153.1 | 1 | |
176 | IL_47732.1 | 1 | |
177 | IL_52509.1 | 1 | |
178 | IL_54470.1 | 1 | tHS tHH bulge with S-turn |
179 | IL_57977.1 | 1 | |
180 | IL_80505.1 | 1 | |
181 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
182 | IL_86059.1 | 1 | |
183 | IL_88119.1 | 1 | |
184 | IL_91044.1 | 1 | |
185 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
186 | IL_98924.1 | 1 | |
187 | IL_02897.1 | 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. |
188 | IL_06847.1 | 1 | Group II Intron IL |
189 | IL_11302.1 | 1 | |
190 | IL_18675.1 | 1 | cWW-bulge-cWW |
191 | IL_25181.1 | 1 | |
192 | IL_28644.1 | 1 | |
193 | IL_41791.1 | 1 | |
194 | IL_52610.1 | 1 | |
195 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
196 | IL_63952.1 | 1 | |
197 | IL_80652.1 | 1 | |
198 | IL_88367.1 | 1 | |
199 | IL_91078.1 | 1 | |
200 | IL_02957.1 | 1 | |
201 | IL_06177.1 | 1 | cWW AG or UU |
202 | IL_30067.1 | 1 | |
203 | IL_46306.1 | 1 | |
204 | IL_55649.1 | 1 | |
205 | IL_58454.1 | 1 | |
206 | IL_64589.1 | 1 | |
207 | IL_69799.1 | 1 | |
208 | IL_77296.1 | 1 | |
209 | IL_81398.1 | 1 | |
210 | IL_83856.1 | 1 | |
211 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
212 | IL_91089.1 | 1 | |
213 | IL_03110.1 | 1 | |
214 | IL_11778.1 | 1 | |
215 | IL_20775.1 | 1 | tSH-inserted |
216 | IL_30354.1 | 1 | |
217 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
218 | IL_37347.1 | 1 | |
219 | IL_49527.1 | 1 | |
220 | IL_52958.1 | 1 | |
221 | IL_83920.1 | 1 | |
222 | IL_89794.1 | 1 | |
223 | IL_91904.1 | 1 | |
224 | IL_97842.1 | 1 | |
225 | IL_03282.1 | 1 | |
226 | IL_06306.1 | 1 | |
227 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
228 | IL_21077.1 | 1 | |
229 | IL_25307.1 | 1 | |
230 | IL_40527.1 | 1 | Kink-turn |
231 | IL_43316.1 | 1 | |
232 | IL_46721.1 | 1 | |
233 | IL_49976.1 | 1 | |
234 | IL_53323.1 | 1 | |
235 | IL_59529.1 | 1 | |
236 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
237 | IL_94973.1 | 1 | Sarcin-Ricin from Group II Intron with inserted base and poor modeling: |
Updated motif groups
# | Motif id | Instances | Description |
---|---|---|---|
1 | IL_97217.9 | 247 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
2 | IL_41766.5 | 52 | Tandem cWW pairs (Not AU or GC) |
3 | IL_28947.2 | 22 | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
4 | IL_46648.5 | 12 | 23S H91 IL | Single-Base Intercalation Site |
5 | IL_25300.2 | 6 | 16S h19 IL and 23S H41 IL |
6 | IL_94403.5 | 4 | LSU H77 |
7 | IL_48918.3 | 4 | Kink-turn variant |
8 | IL_96206.2 | 3 | |
9 | IL_46034.2 | 3 | |
10 | IL_06211.2 | 3 | |
11 | IL_09348.6 | 3 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
12 | IL_09520.3 | 2 | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW |
13 | IL_95150.5 | 2 | |
14 | IL_80348.2 | 2 | 23S H91 IL |
Removed motif groups
# | Motif id | Instances | Description |
---|---|---|---|
1 | IL_39674.1 | 4 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
2 | IL_80433.1 | 2 | |
3 | IL_01054.1 | 2 | |
4 | IL_20530.1 | 1 | |
5 | IL_25314.1 | 1 | |
6 | IL_92280.1 | 1 | |
7 | IL_13682.1 | 1 |
Added motif groups
# | Motif id | Instances | Description |
---|---|---|---|
1 | IL_28003.1 | 3 | |
2 | IL_47475.1 | 2 | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW |
3 | IL_51403.1 | 2 | |
4 | IL_22358.1 | 2 | |
5 | IL_90086.1 | 1 | |
6 | IL_22909.1 | 1 |