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_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_31555.513Tandem sheared with inserted, unpaired purine.
21IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_46648.61323S 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_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_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
27IL_58291.410Recurrent Sub-motif found in junctions
28IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_92114.39GAAA loop receptor "platform" motif
30IL_90459.39cWW AG or UU
31IL_47444.39SRP Loop E-like motif
32IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_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.
34IL_73000.27cHS-cWS
35IL_25300.2616S h19 IL and 23S H41 IL
36IL_25380.16LSU Helix 89 (H89) IL2
37IL_77263.26Kink-turn from U4
38IL_53635.36LSU Helix 32 (H32) IL
39IL_13069.36LSU 3WJ H32-H33-H35A
40IL_90133.36
41IL_72158.36LSU Helix 62 (H62) IL
42IL_08926.3623S H91 IL
43IL_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)
44IL_25230.36Bacterial 5S rRNA Loop E
45IL_70237.36
46IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
47IL_97057.36
48IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
49IL_86357.35LSU Helix 61 IL2
50IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
51IL_79083.35
52IL_02359.35
53IL_39526.44
54IL_48918.34Kink-turn variant
55IL_28572.2416S h18 kink-turn like motif
56IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
57IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
58IL_31066.34SSU Helix 44 (h44) extension
59IL_21333.24tSH-tHW-bulge
60IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
61IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
62IL_39980.14
63IL_98591.34
64IL_01080.14
65IL_82188.24LSU H68 IL from H.m.
66IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67IL_22732.14tSH-inserted-tHS
68IL_38807.34
69IL_31663.1423S H73 ILa : Part of larger Motif
70IL_09530.14Double S-turn motif
71IL_94403.54LSU H77
72IL_42251.14
73IL_34363.24Kink-turn from 23S H42
74IL_45262.44
75IL_62499.73
76IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
77IL_96206.23
78IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
79IL_98421.43SSU Helix 12 (h12) IL
80IL_16166.4323S H91 IL
81IL_05723.13
82IL_43946.13
83IL_28003.13
84IL_06180.13tHS tHH bulge with S-turn
85IL_06211.23
86IL_52173.13
87IL_30840.23
88IL_58586.23
89IL_80494.23LSU H58 IL2 H.m.
90IL_82563.13Thi-box riboswitch T-loop
91IL_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.
92IL_79955.23SSU Helix (23) h23 IL1
93IL_37053.13Kink-turn from 23S H58
94IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
95IL_87065.1323S H91 IL | Single-Base Intercalation Site
96IL_34628.23Kink-turn
97IL_07300.23
98IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
99IL_46034.23
100IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
101IL_11751.12
102IL_77076.12
103IL_98566.12
104IL_31473.12
105IL_45794.12
106IL_65137.12Kink-turn like motif in Group I Intron
107IL_90057.12
108IL_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)
109IL_12211.12
110IL_15840.22Triple Sheared with unpaired, inserted A
111IL_21495.12
112IL_37406.12
113IL_97509.12Double sheared with wobble cWW.
114IL_16330.12
115IL_87507.12tHS tHH bulge with S-turn
116IL_31707.12Vitamin B12 aptamer
117IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
118IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
119IL_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)
120IL_90735.12
121IL_40892.12
122IL_33964.12
123IL_97833.12
124IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
125IL_23262.42
126IL_69536.12LSU Helix 96 (H96) IL2
127IL_94744.12Sarcin-ricin motif with extra cWW GA pair
128IL_76095.32Motif from Hairpin Ribozyme
129IL_80093.12
130IL_30381.12tHS tHH bulge with S-turn
131IL_95884.12
132IL_23414.12
133IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
134IL_50521.12
135IL_22358.12
136IL_80348.2223S H91 IL
137IL_87548.12
138IL_09587.12
139IL_00998.12
140IL_67887.12
141IL_21639.12
142IL_70401.12
143IL_52940.12
144IL_09882.12
145IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
146IL_46435.12
147IL_95150.52
148IL_37197.12
149IL_33842.12
150IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
151IL_43316.11
152IL_12507.11
153IL_69799.11
154IL_47687.11
155IL_52958.11
156IL_06808.11Double sheared (tSH-tSH) one bulged base.
157IL_91078.11
158IL_83856.11
159IL_76486.11Sarcin-ricin motif with syn G
160IL_57364.11LSU Helix 89 (H89) IL2
161IL_41139.11
162IL_91044.11
163IL_87394.11
164IL_05513.11
165IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
166IL_34076.11
167IL_80505.11
168IL_22909.11
169IL_80652.11
170IL_54450.11
171IL_71942.11
172IL_81398.11
173IL_97842.11
174IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
175IL_64589.11
176IL_54470.11tHS tHH bulge with S-turn
177IL_06847.11Group II Intron IL
178IL_42891.11
179IL_40845.11
180IL_06177.11cWW AG or UU
181IL_82650.11
182IL_26868.11
183IL_55649.11
184IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
185IL_27503.11
186IL_37347.11
187IL_46306.11
188IL_82601.11Tandem cWW water-inserted CU pairs
189IL_91089.11
190IL_60649.11Kink-turn
191IL_47732.11
192IL_02835.11
193IL_25307.11
194IL_11302.11
195IL_31224.1123S H91 IL
196IL_05221.11
197IL_06471.11
198IL_68767.11
199IL_17603.11
200IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
201IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
202IL_77296.11
203IL_30354.11
204IL_50911.1116S h34 ILa : Part of larger motif
205IL_03110.11
206IL_41791.11
207IL_76263.11
208IL_66744.11SSU Helix 21 (h21) IL2 E.coli
209IL_89794.11
210IL_28644.11
211IL_52509.11
212IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
213IL_25082.11
214IL_53323.11
215IL_26971.11
216IL_56513.11
217IL_15205.11
218IL_87523.11
219IL_03282.11
220IL_46721.11
221IL_85805.11
222IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
223IL_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.
224IL_68827.11Reverse Kink-Turn
225IL_83920.11
226IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
227IL_53988.11
228IL_61730.11
229IL_75415.11Pseudo-knot forming internal loop
230IL_88119.11
231IL_98924.11
232IL_59529.11
233IL_91904.11
234IL_21421.11
235IL_85510.11
236IL_21077.11
237IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
238IL_41153.11
239IL_83250.1116S h40 3WJ T.th.
240IL_57977.11
241IL_39324.11
242IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
243IL_11778.11
244IL_71685.11Sarcin-like with an intercalated basepair
245IL_25181.11
246IL_09491.11
247IL_58454.11
248IL_88367.11
249IL_49527.11
250IL_30067.11
251IL_63952.11
252IL_86059.11
253IL_06468.1116S h40 3WJ E.c.
254IL_91956.11
255IL_06421.11Single sheared with bulged bases
256IL_20775.11tSH-inserted
257IL_03741.11
258IL_06306.11
259IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
260IL_23639.11tWH-tHS-L-cWW
261IL_02957.11
262IL_18675.11cWW-bulge-cWW
263IL_40527.11Kink-turn
264IL_49976.11
265IL_52610.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription