Changes in PDB files used for clustering

Release 1.6 has 203 PDB files, release 1.7 has 203 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

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

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Changes in motif groups

Release 1.6 has 272 motif groups, release 1.7 has 272 motif groups, 272 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.6, 0 groups are only in release 1.7.

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_97217.72431-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.8205cWW AG or water inserted cWW Y-Y.
3IL_39199.453Hoogsteen-edge Platform, Single bulged base
4IL_41766.449Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.443Sugar-edge, 1-base platform, consensus tHS
7IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_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
9IL_13959.426Double Sheared (tSH-tHS)
10IL_65553.722Kink-turn
11IL_93424.421tSH-inserted-tHW
12IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
13IL_73276.421C-loop
14IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_94430.51616S h32-h33-h34 3WJ
17IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
18IL_85647.316Sarcin-ricin parent motif with 15 Nts
19IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_31555.413Tandem sheared with inserted, unpaired purine.
22IL_46648.41123S H91 IL | Single-Base Intercalation Site
23IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
25IL_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
26IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_58291.410Recurrent Sub-motif found in junctions
28IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_47444.39SRP Loop E-like motif
30IL_90459.39cWW AG or UU
31IL_92114.39GAAA loop receptor "platform" motif
32IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_73000.27cHS-cWS
34IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
35IL_25230.36Bacterial 5S rRNA Loop E
36IL_70237.36
37IL_13069.36LSU 3WJ H32-H33-H35A
38IL_97057.36
39IL_53635.36LSU Helix 32 (H32) IL
40IL_08926.3623S H91 IL
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_90133.36
43IL_25380.16LSU Helix 89 (H89) IL2
44IL_72158.36LSU Helix 62 (H62) IL
45IL_77263.26Kink-turn from U4
46IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
47IL_86357.35LSU Helix 61 IL2
48IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
49IL_79083.35
50IL_25300.1516S h19 IL and 23S H41 IL
51IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
52IL_02359.35
53IL_22732.14tSH-inserted-tHS
54IL_28572.2416S h18 kink-turn like motif
55IL_09530.14Double S-turn motif
56IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
57IL_31663.1423S H73 ILa : Part of larger Motif
58IL_82188.24LSU H68 IL from H.m.
59IL_94403.34LSU H77
60IL_39526.44
61IL_45262.44
62IL_98591.34
63IL_21333.24tSH-tHW-bulge
64IL_39980.14
65IL_42251.14
66IL_01080.14
67IL_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)
68IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
69IL_31066.34SSU Helix 44 (h44) extension
70IL_34363.24Kink-turn from 23S H42
71IL_38807.34
72IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
73IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
74IL_16166.4323S H91 IL
75IL_34628.23Kink-turn
76IL_43946.13
77IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
78IL_05723.13
79IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
80IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
81IL_58586.23
82IL_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.
83IL_98421.43SSU Helix 12 (h12) IL
84IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
85IL_37053.13Kink-turn from 23S H58
86IL_75447.13
87IL_79955.23SSU Helix (23) h23 IL1
88IL_87065.1323S H91 IL | Single-Base Intercalation Site
89IL_06180.13tHS tHH bulge with S-turn
90IL_07300.23
91IL_06211.13
92IL_80348.1323S H91 IL
93IL_82563.13Thi-box riboswitch T-loop
94IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
95IL_52173.13
96IL_30840.23
97IL_62499.73
98IL_80494.23LSU H58 IL2 H.m.
99IL_95150.43
100IL_48918.23Kink-turn variant
101IL_12211.12
102IL_40892.12
103IL_52940.12
104IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
105IL_16330.12
106IL_23262.42
107IL_65137.12Kink-turn like motif in Group I Intron
108IL_96206.12
109IL_09587.12
110IL_23414.12
111IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
112IL_98566.12
113IL_09882.12
114IL_31707.12Vitamin B12 aptamer
115IL_50521.12
116IL_76095.32Motif from Hairpin Ribozyme
117IL_80093.12
118IL_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)
119IL_87507.12tHS tHH bulge with S-turn
120IL_90057.12
121IL_00998.12
122IL_37197.12
123IL_45794.12
124IL_67887.12
125IL_94744.12Sarcin-ricin motif with extra cWW GA pair
126IL_01054.12
127IL_30381.12tHS tHH bulge with S-turn
128IL_46034.12
129IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
130IL_77076.12
131IL_80433.12
132IL_87548.12
133IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
134IL_11751.12
135IL_21495.12
136IL_33964.12
137IL_37406.12
138IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
139IL_90735.12
140IL_97509.12Double sheared with wobble cWW.
141IL_15840.22Triple Sheared with unpaired, inserted A
142IL_19898.12
143IL_21639.12
144IL_46435.12
145IL_69536.12LSU Helix 96 (H96) IL2
146IL_97833.12
147IL_06471.11
148IL_20530.11
149IL_31224.1123S H91 IL
150IL_55649.11
151IL_58454.11
152IL_64589.11
153IL_69799.11
154IL_80652.11
155IL_88367.11
156IL_91078.11
157IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
158IL_97842.11
159IL_02835.11
160IL_06808.11Double sheared (tSH-tSH) one bulged base.
161IL_12507.11
162IL_20775.11tSH-inserted
163IL_28644.11
164IL_39324.11
165IL_41139.11
166IL_46721.11
167IL_49527.11
168IL_52958.11
169IL_75415.11Pseudo-knot forming internal loop
170IL_81398.11
171IL_83856.11
172IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
173IL_91089.11
174IL_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.
175IL_06177.11cWW AG or UU
176IL_06847.11Group II Intron IL
177IL_21077.11
178IL_41153.11
179IL_49976.11
180IL_53323.11
181IL_59529.11
182IL_83920.11
183IL_89794.11
184IL_91904.11
185IL_02957.11
186IL_13682.11
187IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
188IL_23639.11tWH-tHS-L-cWW
189IL_25307.11
190IL_30067.11
191IL_56513.11
192IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
193IL_66744.11SSU Helix 21 (h21) IL2 E.coli
194IL_71685.11Sarcin-like with an intercalated basepair
195IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
196IL_03110.11
197IL_10365.11
198IL_17603.11
199IL_25314.11
200IL_30354.11
201IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
202IL_41791.11
203IL_47687.11
204IL_50911.1116S h34 ILa : Part of larger motif
205IL_53988.11
206IL_57364.11LSU Helix 89 (H89) IL2
207IL_60649.11Kink-turn
208IL_71942.11
209IL_76486.11Sarcin-ricin motif with syn G
210IL_85510.11
211IL_87523.11
212IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
213IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
214IL_03282.11
215IL_06306.11
216IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
217IL_11302.11
218IL_15205.11
219IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
220IL_21421.11
221IL_37347.11
222IL_47732.11
223IL_54450.11
224IL_61730.11
225IL_68767.11
226IL_82601.11Tandem cWW water-inserted CU pairs
227IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
228IL_98924.11
229IL_03741.11
230IL_06421.11Single sheared with bulged bases
231IL_18675.11cWW-bulge-cWW
232IL_25082.11
233IL_26868.11
234IL_40527.11Kink-turn
235IL_46306.11
236IL_52509.11
237IL_54470.11tHS tHH bulge with S-turn
238IL_57977.11
239IL_82650.11
240IL_85805.11
241IL_92280.11
242IL_05221.11
243IL_06468.1116S h40 3WJ E.c.
244IL_09491.11
245IL_11778.11
246IL_25181.11
247IL_26971.11
248IL_40845.11
249IL_43316.11
250IL_52610.11
251IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
252IL_63952.11
253IL_77296.11
254IL_80505.11
255IL_83250.1116S h40 3WJ T.th.
256IL_86059.11
257IL_88119.11
258IL_91044.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription