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

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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 idInstancesDescription
1IL_47174.8205cWW AG or water inserted cWW Y-Y.
2IL_39199.453Hoogsteen-edge Platform, Single bulged base
3IL_56465.346Single, unpaired intercalated base, consensus A
4IL_44540.443Sugar-edge, 1-base platform, consensus tHS
5IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
6IL_82444.129cWH 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
7IL_13959.426Double Sheared (tSH-tHS)
8IL_73276.522C-loop
9IL_65553.722Kink-turn
10IL_93424.421tSH-inserted-tHW
11IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
12IL_92027.31716S h21 S8 binding site
13IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
14IL_94430.51616S h32-h33-h34 3WJ
15IL_85647.316Sarcin-ricin parent motif with 15 Nts
16IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
17IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_31555.413Tandem sheared with inserted, unpaired purine.
19IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
20IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21IL_58291.410Recurrent Sub-motif found in junctions
22IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_17212.110cWW 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
24IL_90459.39cWW AG or UU
25IL_47444.39SRP Loop E-like motif
26IL_92114.39GAAA loop receptor "platform" motif
27IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_73000.27cHS-cWS
29IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
30IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31IL_25230.36Bacterial 5S rRNA Loop E
32IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
33IL_70237.36
34IL_97057.36
35IL_77263.26Kink-turn from U4
36IL_25380.16LSU Helix 89 (H89) IL2
37IL_53635.36LSU Helix 32 (H32) IL
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_90133.36
40IL_72158.36LSU Helix 62 (H62) IL
41IL_08926.3623S H91 IL
42IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
43IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
44IL_79083.35
45IL_02359.35
46IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_86357.35LSU Helix 61 IL2
48IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
49IL_21333.24tSH-tHW-bulge
50IL_39980.14
51IL_98591.34
52IL_82188.24LSU H68 IL from H.m.
53IL_28572.2416S h18 kink-turn like motif
54IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
55IL_31066.34SSU Helix 44 (h44) extension
56IL_38807.34
57IL_31663.1423S H73 ILa : Part of larger Motif
58IL_01080.14
59IL_42251.14
60IL_34363.24Kink-turn from 23S H42
61IL_45262.44
62IL_09530.14Double S-turn motif
63IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
64IL_22732.14tSH-inserted-tHS
65IL_39526.44
66IL_15709.14Single 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)
67IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
68IL_05723.13
69IL_62499.73
70IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
71IL_58586.23
72IL_80494.23LSU H58 IL2 H.m.
73IL_89028.63Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
74IL_34628.23Kink-turn
75IL_52173.13
76IL_37053.13Kink-turn from 23S H58
77IL_75447.13
78IL_87065.1323S H91 IL | Single-Base Intercalation Site
79IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
80IL_98421.43SSU Helix 12 (h12) IL
81IL_82563.13Thi-box riboswitch T-loop
82IL_06180.13tHS tHH bulge with S-turn
83IL_30840.23
84IL_43946.13
85IL_79955.23SSU Helix (23) h23 IL1
86IL_16166.4323S H91 IL
87IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
88IL_07300.23
89IL_52940.12
90IL_65137.12Kink-turn like motif in Group I Intron
91IL_46435.12
92IL_23262.42
93IL_69536.12LSU Helix 96 (H96) IL2
94IL_45794.12
95IL_87507.12tHS tHH bulge with S-turn
96IL_11751.12
97IL_97833.12
98IL_80093.12
99IL_15840.22Triple Sheared with unpaired, inserted A
100IL_16330.12
101IL_33964.12
102IL_76095.32Motif from Hairpin Ribozyme
103IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
104IL_97509.12Double sheared with wobble cWW.
105IL_40892.12
106IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
107IL_00998.12
108IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
109IL_90735.12
110IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
111IL_77076.12
112IL_12211.12
113IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
114IL_90057.12
115IL_98566.12
116IL_30381.12tHS tHH bulge with S-turn
117IL_23414.12
118IL_31707.12Vitamin B12 aptamer
119IL_50521.12
120IL_09882.12
121IL_85015.1223S 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)
122IL_09587.12
123IL_37406.12
124IL_87548.12
125IL_19898.12
126IL_21495.12
127IL_94744.12Sarcin-ricin motif with extra cWW GA pair
128IL_67887.12
129IL_21639.12
130IL_37197.12
131IL_63952.11
132IL_02835.11
133IL_47687.11
134IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
135IL_03741.11
136IL_06306.11
137IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
138IL_23639.11tWH-tHS-L-cWW
139IL_64589.11
140IL_54470.11tHS tHH bulge with S-turn
141IL_60649.11Kink-turn
142IL_46721.11
143IL_03110.11
144IL_41791.11
145IL_12507.11
146IL_69799.11
147IL_89794.11
148IL_28644.11
149IL_52509.11
150IL_61730.11
151IL_91078.11
152IL_83856.11
153IL_76486.11Sarcin-ricin motif with syn G
154IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
155IL_82601.11Tandem cWW water-inserted CU pairs
156IL_91089.11
157IL_77296.11
158IL_41153.11
159IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
160IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
161IL_02897.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
162IL_80505.11
163IL_26868.11
164IL_53988.11
165IL_81398.11
166IL_97842.11
167IL_46306.11
168IL_17603.11
169IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
170IL_87523.11
171IL_03282.11
172IL_05513.11
173IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
174IL_40845.11
175IL_57977.11
176IL_39324.11
177IL_43316.11
178IL_82650.11
179IL_11302.11
180IL_11778.11
181IL_37347.11
182IL_06471.11
183IL_68767.11
184IL_56513.11
185IL_15205.11
186IL_21077.11
187IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
188IL_86059.11
189IL_25307.11
190IL_66744.11SSU Helix 21 (h21) IL2 E.coli
191IL_06421.11Single sheared with bulged bases
192IL_20775.11tSH-inserted
193IL_71942.11
194IL_31224.1123S H91 IL
195IL_05221.11
196IL_26971.11
197IL_21421.11
198IL_85510.11
199IL_49527.11
200IL_30067.11
201IL_50911.1116S h34 ILa : Part of larger motif
202IL_06177.11cWW AG or UU
203IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
204IL_52958.11
205IL_06808.11Double sheared (tSH-tSH) one bulged base.
206IL_25082.11
207IL_53323.11
208IL_59529.11
209IL_91904.11
210IL_58454.11
211IL_88367.11
212IL_49976.11
213IL_52610.11
214IL_85805.11
215IL_83920.11
216IL_80652.11
217IL_54450.11
218IL_75415.11Pseudo-knot forming internal loop
219IL_88119.11
220IL_98924.11
221IL_25181.11
222IL_09491.11
223IL_18675.11cWW-bulge-cWW
224IL_40527.11Kink-turn
225IL_91044.11
226IL_47732.11
227IL_83250.1116S h40 3WJ T.th.
228IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
229IL_06468.1116S h40 3WJ E.c.
230IL_55649.11
231IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
232IL_71685.11Sarcin-like with an intercalated basepair
233IL_02957.11
234IL_57364.11LSU Helix 89 (H89) IL2
235IL_41139.11
236IL_06847.11Group II Intron IL
237IL_30354.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.92471-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_41766.552Tandem cWW pairs (Not AU or GC)
3IL_28947.22223S 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
4IL_46648.51223S H91 IL | Single-Base Intercalation Site
5IL_25300.2616S h19 IL and 23S H41 IL
6IL_48918.34Kink-turn variant
7IL_94403.54LSU H77
8IL_96206.23
9IL_46034.23
10IL_06211.23
11IL_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
12IL_95150.52
13IL_80348.2223S H91 IL
14IL_09520.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW

Removed motif groups

#Motif idInstancesDescription
1IL_39674.14LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_80433.12
3IL_01054.12
4IL_25314.11
5IL_92280.11
6IL_13682.11
7IL_20530.11

Added motif groups

#Motif idInstancesDescription
1IL_28003.13
2IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_51403.12
4IL_22358.12
5IL_90086.11
6IL_22909.11