Changes in PDB files used for clustering

Release 1.10 has 214 PDB files, release 1.11 has 214 PDB files, 214 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 1.10 has 275 motif groups, release 1.11 has 275 motif groups, 275 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.10, 0 groups are only in release 1.11.

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_97217.102481-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.9208cWW AG or water inserted cWW Y-Y.
3IL_41766.654Tandem cWW pairs (Not AU or GC)
4IL_39199.453Hoogsteen-edge Platform, Single bulged base
5IL_56465.447Single, 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_73276.522C-loop
12IL_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
13IL_93424.421tSH-inserted-tHW
14IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_94430.51616S h32-h33-h34 3WJ
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_46648.61323S H91 IL | Single-Base Intercalation Site
22IL_31555.513Tandem sheared with inserted, unpaired purine.
23IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_58291.410Recurrent Sub-motif found in junctions
27IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
28IL_92114.39GAAA loop receptor "platform" motif
29IL_90459.39cWW AG or UU
30IL_47444.39SRP Loop E-like motif
31IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_46301.17Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_73000.27cHS-cWS
35IL_53635.36LSU Helix 32 (H32) IL
36IL_13069.36LSU 3WJ H32-H33-H35A
37IL_90133.36
38IL_72158.36LSU Helix 62 (H62) IL
39IL_08926.3623S H91 IL
40IL_25380.16LSU Helix 89 (H89) IL2
41IL_70173.16Single 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)
42IL_25230.36Bacterial 5S rRNA Loop E
43IL_70237.36
44IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45IL_25300.2616S h19 IL and 23S H41 IL
46IL_97057.36
47IL_77263.26Kink-turn from U4
48IL_02359.35
49IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
50IL_79083.35
51IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
52IL_86357.35LSU Helix 61 IL2
53IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
54IL_31066.34SSU Helix 44 (h44) extension
55IL_21333.24tSH-tHW-bulge
56IL_39526.44
57IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
58IL_01080.14
59IL_39980.14
60IL_98591.34
61IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
62IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
63IL_82188.24LSU H68 IL from H.m.
64IL_48918.34Kink-turn variant
65IL_22732.14tSH-inserted-tHS
66IL_94403.54LSU H77
67IL_38807.34
68IL_31663.1423S H73 ILa : Part of larger Motif
69IL_42251.14
70IL_34363.24Kink-turn from 23S H42
71IL_45262.44
72IL_09530.14Double S-turn motif
73IL_28572.2416S h18 kink-turn like motif
74IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
75IL_96206.23
76IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
77IL_34628.23Kink-turn
78IL_30840.23
79IL_98421.43SSU Helix 12 (h12) IL
80IL_16166.4323S H91 IL
81IL_06211.23
82IL_52173.13
83IL_05723.13
84IL_43946.13
85IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
86IL_07300.23
87IL_79955.23SSU Helix (23) h23 IL1
88IL_58586.23
89IL_80494.23LSU H58 IL2 H.m.
90IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
91IL_46034.23
92IL_37053.13Kink-turn from 23S H58
93IL_82563.13Thi-box riboswitch T-loop
94IL_62499.73
95IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
96IL_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.
97IL_87065.1323S H91 IL | Single-Base Intercalation Site
98IL_28003.13
99IL_06180.13tHS tHH bulge with S-turn
100IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
101IL_31707.12Vitamin B12 aptamer
102IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
103IL_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)
104IL_12211.12
105IL_23414.12
106IL_97833.12
107IL_15840.22Triple Sheared with unpaired, inserted A
108IL_21495.12
109IL_95150.52
110IL_80348.2223S H91 IL
111IL_76095.32Motif from Hairpin Ribozyme
112IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
113IL_37406.12
114IL_67887.12
115IL_21639.12
116IL_37197.12
117IL_50521.12
118IL_22358.12
119IL_80093.12
120IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
121IL_45794.12
122IL_96446.12
123IL_87548.12
124IL_30381.12tHS tHH bulge with S-turn
125IL_95884.12
126IL_23262.42
127IL_69536.12LSU Helix 96 (H96) IL2
128IL_94744.12Sarcin-ricin motif with extra cWW GA pair
129IL_31473.12
130IL_87507.12tHS tHH bulge with S-turn
131IL_52940.12
132IL_09882.12
133IL_97509.12Double sheared with wobble cWW.
134IL_16330.12
135IL_40892.12
136IL_33964.12
137IL_70401.12
138IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
139IL_11751.12
140IL_77076.12
141IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
142IL_46435.12
143IL_09587.12
144IL_43877.12Single 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) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
145IL_90735.12
146IL_33842.12
147IL_65137.12Kink-turn like motif in Group I Intron
148IL_90057.12
149IL_98566.12
150IL_00998.12
151IL_26971.11
152IL_56513.11
153IL_15205.11
154IL_87523.11
155IL_77296.11
156IL_87394.11
157IL_05513.11
158IL_40845.11
159IL_80505.11
160IL_69799.11
161IL_47687.11
162IL_06421.11Single sheared with bulged bases
163IL_20775.11tSH-inserted
164IL_25082.11
165IL_53323.11
166IL_59529.11
167IL_91904.11
168IL_21421.11
169IL_85510.11
170IL_21077.11
171IL_03282.11
172IL_42891.11
173IL_06177.11cWW AG or UU
174IL_82650.11
175IL_22909.11
176IL_52958.11
177IL_06808.11Double sheared (tSH-tSH) one bulged base.
178IL_75415.11Pseudo-knot forming internal loop
179IL_88119.11
180IL_98924.11
181IL_25181.11
182IL_09491.11
183IL_58454.11
184IL_88367.11
185IL_49527.11
186IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
187IL_47732.11
188IL_50911.1116S h34 ILa : Part of larger motif
189IL_88865.11
190IL_02835.11
191IL_25307.11
192IL_26868.11
193IL_80652.11
194IL_54450.11
195IL_71685.11Sarcin-like with an intercalated basepair
196IL_02957.11
197IL_18675.11cWW-bulge-cWW
198IL_40527.11Kink-turn
199IL_49976.11
200IL_57285.11
201IL_30354.11
202IL_85805.11
203IL_03110.11
204IL_41791.11
205IL_76263.11
206IL_91379.11
207IL_11302.11
208IL_31006.11tSH-tHW-L-bif-cWW
209IL_55649.11
210IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
211IL_77014.11
212IL_03741.11
213IL_06306.11
214IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
215IL_23639.11tWH-tHS-L-cWW
216IL_57364.11LSU Helix 89 (H89) IL2
217IL_41139.11
218IL_23448.11
219IL_46721.11
220IL_83250.1116S h40 3WJ T.th.
221IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
222IL_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.
223IL_68827.11Reverse Kink-Turn
224IL_66744.11SSU Helix 21 (h21) IL2 E.coli
225IL_71942.11
226IL_91078.11
227IL_83856.11
228IL_76486.11Sarcin-ricin motif with syn G
229IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
230IL_64589.11
231IL_54470.11tHS tHH bulge with S-turn
232IL_91044.11
233IL_27668.11
234IL_41153.11
235IL_63952.11
236IL_57977.11
237IL_39324.11
238IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
239IL_83920.11
240IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
241IL_89794.11
242IL_28644.11
243IL_52509.11
244IL_27243.11
245IL_75328.11
246IL_81398.11
247IL_97842.11
248IL_82601.11Tandem cWW water-inserted CU pairs
249IL_91089.11
250IL_06847.11Group II Intron IL
251IL_30067.11
252IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
253IL_86059.11
254IL_53988.11
255IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
256IL_27503.11
257IL_37347.11
258IL_46306.11
259IL_68767.11
260IL_17603.11
261IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
262IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
263IL_60649.11Kink-turn
264IL_52610.11
265IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
266IL_34076.11
267IL_43316.11
268IL_12507.11
269IL_06468.1116S h40 3WJ E.c.
270IL_91956.11
271IL_11778.11
272IL_61730.11
273IL_31224.1123S H91 IL
274IL_05221.11
275IL_06471.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription