Changes in PDB files used for clustering

Release 1.10 has 213 PDB files, release 1.11 has 213 PDB files, 213 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_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
12IL_73276.522C-loop
13IL_93424.421tSH-inserted-tHW
14IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_94430.51616S h32-h33-h34 3WJ
17IL_85647.316Sarcin-ricin parent motif with 15 Nts
18IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
20IL_31555.513Tandem sheared with inserted, unpaired purine.
21IL_46648.61323S H91 IL | Single-Base Intercalation Site
22IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
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_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_58291.410Recurrent Sub-motif found in junctions
28IL_47444.39SRP Loop E-like motif
29IL_90459.39cWW AG or UU
30IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_92114.39GAAA loop receptor "platform" motif
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_25230.36Bacterial 5S rRNA Loop E
36IL_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)
37IL_08926.3623S H91 IL
38IL_53635.36LSU Helix 32 (H32) IL
39IL_70237.36
40IL_97057.36
41IL_25300.2616S h19 IL and 23S H41 IL
42IL_90133.36
43IL_13069.36LSU 3WJ H32-H33-H35A
44IL_25380.16LSU Helix 89 (H89) IL2
45IL_72158.36LSU Helix 62 (H62) IL
46IL_77263.26Kink-turn from U4
47IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
48IL_79083.35
49IL_02359.35
50IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
51IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
52IL_86357.35LSU Helix 61 IL2
53IL_31066.34SSU Helix 44 (h44) extension
54IL_39980.14
55IL_42251.14
56IL_94403.54LSU H77
57IL_28572.2416S h18 kink-turn like motif
58IL_82188.24LSU H68 IL from H.m.
59IL_01080.14
60IL_21333.24tSH-tHW-bulge
61IL_34363.24Kink-turn from 23S H42
62IL_38807.34
63IL_98591.34
64IL_09530.14Double S-turn motif
65IL_31663.1423S H73 ILa : Part of larger Motif
66IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
67IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
68IL_48918.34Kink-turn variant
69IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
70IL_39526.44
71IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
72IL_22732.14tSH-inserted-tHS
73IL_45262.44
74IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
75IL_06180.13tHS tHH bulge with S-turn
76IL_07300.23
77IL_16166.4323S H91 IL
78IL_28003.13
79IL_58586.23
80IL_87065.1323S H91 IL | Single-Base Intercalation Site
81IL_96206.23
82IL_98421.43SSU Helix 12 (h12) IL
83IL_06211.23
84IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
85IL_46034.23
86IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
87IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
88IL_79955.23SSU Helix (23) h23 IL1
89IL_34628.23Kink-turn
90IL_52173.13
91IL_82563.13Thi-box riboswitch T-loop
92IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
93IL_43946.13
94IL_37053.13Kink-turn from 23S H58
95IL_62499.73
96IL_80494.23LSU H58 IL2 H.m.
97IL_05723.13
98IL_30840.23
99IL_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.
100IL_11751.12
101IL_33964.12
102IL_45794.12
103IL_65137.12Kink-turn like motif in Group I Intron
104IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
105IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
106IL_00998.12
107IL_16330.12
108IL_23262.42
109IL_37406.12
110IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
111IL_50521.12
112IL_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)
113IL_87507.12tHS tHH bulge with S-turn
114IL_90057.12
115IL_98566.12
116IL_12211.12
117IL_23414.12
118IL_31473.12
119IL_70401.12
120IL_94744.12Sarcin-ricin motif with extra cWW GA pair
121IL_40892.12
122IL_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)
123IL_67887.12
124IL_76095.32Motif from Hairpin Ribozyme
125IL_80093.12
126IL_87548.12
127IL_21495.12
128IL_46435.12
129IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
130IL_80348.2223S H91 IL
131IL_90735.12
132IL_95150.52
133IL_09587.12
134IL_21639.12
135IL_31707.12Vitamin B12 aptamer
136IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
137IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
138IL_77076.12
139IL_97509.12Double sheared with wobble cWW.
140IL_09882.12
141IL_22358.12
142IL_30381.12tHS tHH bulge with S-turn
143IL_52940.12
144IL_69536.12LSU Helix 96 (H96) IL2
145IL_95884.12
146IL_97833.12
147IL_15840.22Triple Sheared with unpaired, inserted A
148IL_33842.12
149IL_37197.12
150IL_03110.11
151IL_21077.11
152IL_22909.11
153IL_37347.11
154IL_49976.11
155IL_53323.11
156IL_81398.11
157IL_83920.11
158IL_89794.11
159IL_91904.11
160IL_03282.11
161IL_11778.11
162IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
163IL_31224.1123S H91 IL
164IL_34076.11
165IL_40527.11Kink-turn
166IL_59529.11
167IL_91956.11
168IL_03741.11
169IL_06306.11
170IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
171IL_28644.11
172IL_40845.11
173IL_43316.11
174IL_47687.11
175IL_50911.1116S h34 ILa : Part of larger motif
176IL_53988.11
177IL_56513.11
178IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
179IL_66744.11SSU Helix 21 (h21) IL2 E.coli
180IL_75415.11Pseudo-knot forming internal loop
181IL_85510.11
182IL_87523.11
183IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
184IL_05221.11
185IL_06421.11Single sheared with bulged bases
186IL_09491.11
187IL_12507.11
188IL_21421.11
189IL_23639.11tWH-tHS-L-cWW
190IL_25307.11
191IL_46306.11
192IL_47732.11
193IL_54450.11
194IL_57364.11LSU Helix 89 (H89) IL2
195IL_60649.11Kink-turn
196IL_71685.11Sarcin-like with an intercalated basepair
197IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
198IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
199IL_05513.11
200IL_06468.1116S h40 3WJ E.c.
201IL_17603.11
202IL_30067.11
203IL_39324.11
204IL_41139.11
205IL_52509.11
206IL_54470.11tHS tHH bulge with S-turn
207IL_61730.11
208IL_68767.11
209IL_71942.11
210IL_76486.11Sarcin-ricin motif with syn G
211IL_82601.11Tandem cWW water-inserted CU pairs
212IL_85805.11
213IL_98924.11
214IL_02835.11
215IL_06471.11
216IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
217IL_26868.11
218IL_30354.11
219IL_41153.11
220IL_52610.11
221IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
222IL_57977.11
223IL_82650.11
224IL_86059.11
225IL_88119.11
226IL_91044.11
227IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
228IL_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.
229IL_06808.11Double sheared (tSH-tSH) one bulged base.
230IL_15205.11
231IL_18675.11cWW-bulge-cWW
232IL_25082.11
233IL_26971.11
234IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
235IL_46721.11
236IL_63952.11
237IL_80505.11
238IL_83250.1116S h40 3WJ T.th.
239IL_88367.11
240IL_91078.11
241IL_02957.11
242IL_06177.11cWW AG or UU
243IL_06847.11Group II Intron IL
244IL_11302.11
245IL_20775.11tSH-inserted
246IL_25181.11
247IL_27503.11
248IL_41791.11
249IL_49527.11
250IL_52958.11
251IL_55649.11
252IL_58454.11
253IL_64589.11
254IL_69799.11
255IL_77296.11
256IL_80652.11
257IL_83856.11
258IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
259IL_91089.11
260IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
261IL_97842.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription