Changes in PDB files used for clustering

Release 1.12 has 217 PDB files, release 1.13 has 219 PDB files, 216 of them are identical.

1 equivalence classes changed representatives: 3SD34LVZ.

2 new structures in release 1.13: 4JK0, 4NGF.

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

Loading the Sankey diagram...

Changes in motif groups

Release 1.12 has 276 motif groups, release 1.13 has 278 motif groups, 271 of them are identical.

2 motif groups were updated, 3 groups are present only in release 1.12, 5 groups are only in release 1.13.

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_41766.654Tandem cWW pairs (Not AU or GC)
2IL_39199.453Hoogsteen-edge Platform, Single bulged base
3IL_56465.447Single, 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_65553.823Kink-turn
9IL_73276.522C-loop
10IL_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
11IL_93424.421tSH-inserted-tHW
12IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.31716S h21 S8 binding site
14IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
15IL_94430.51616S h32-h33-h34 3WJ
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_46648.61323S H91 IL | Single-Base Intercalation Site
19IL_31555.513Tandem sheared with inserted, unpaired purine.
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
22IL_37104.311Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 23S 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)
23IL_17212.211cWW 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_58291.410Recurrent Sub-motif found in junctions
25IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_90459.39cWW AG or UU
28IL_92114.39GAAA loop receptor "platform" motif
29IL_47444.39SRP Loop E-like motif
30IL_73000.27cHS-cWS
31IL_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.
32IL_25300.3716S h19 IL and 23S H41 IL
33IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_13069.36LSU 3WJ H32-H33-H35A
35IL_90133.36
36IL_72158.36LSU Helix 62 (H62) IL
37IL_70237.36
38IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
39IL_25230.36Bacterial 5S rRNA Loop E
40IL_25380.16LSU Helix 89 (H89) IL2
41IL_97057.36
42IL_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)
43IL_77263.26Kink-turn from U4
44IL_53635.36LSU Helix 32 (H32) IL
45IL_08926.3623S H91 IL
46IL_79083.35
47IL_02359.35
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_31066.34SSU Helix 44 (h44) extension
52IL_39980.14
53IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
54IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
55IL_98591.34
56IL_01080.14
57IL_82188.24LSU H68 IL from H.m.
58IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
59IL_09530.14Double S-turn motif
60IL_48918.34Kink-turn variant
61IL_22732.14tSH-inserted-tHS
62IL_94403.54LSU H77
63IL_42251.14
64IL_38807.34
65IL_31663.1423S H73 ILa : Part of larger Motif
66IL_39526.44
67IL_34363.24Kink-turn from 23S H42
68IL_45262.44
69IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
70IL_28572.2416S h18 kink-turn like motif
71IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
72IL_21333.24tSH-tHW-bulge
73IL_80348.3323S H91 IL
74IL_47875.13LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
75IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
76IL_16166.4323S H91 IL
77IL_43946.13
78IL_98421.43SSU Helix 12 (h12) IL
79IL_05723.13
80IL_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.
81IL_07300.23
82IL_06211.33
83IL_52173.13
84IL_58586.23
85IL_82563.13Thi-box riboswitch T-loop
86IL_87065.1323S H91 IL | Single-Base Intercalation Site
87IL_34628.23Kink-turn
88IL_80494.23LSU H58 IL2 H.m.
89IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
90IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
91IL_79955.23SSU Helix (23) h23 IL1
92IL_37053.13Kink-turn from 23S H58
93IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
94IL_95150.63
95IL_62499.73
96IL_28003.13
97IL_06180.13tHS tHH bulge with S-turn
98IL_30840.23
99IL_31707.12Vitamin B12 aptamer
100IL_97833.12
101IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
102IL_24293.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 23S 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)
103IL_46034.32
104IL_76095.32Motif from Hairpin Ribozyme
105IL_30381.12tHS tHH bulge with S-turn
106IL_31039.12
107IL_67887.12
108IL_21639.12
109IL_70401.12
110IL_80093.12
111IL_00998.12
112IL_37197.12
113IL_33842.12
114IL_50521.12
115IL_09587.12
116IL_97509.12Double sheared with wobble cWW.
117IL_45794.12
118IL_87548.12
119IL_96206.32
120IL_46435.12
121IL_16330.12
122IL_87507.12tHS tHH bulge with S-turn
123IL_52940.12
124IL_09882.12
125IL_77076.12
126IL_21495.12
127IL_37406.12
128IL_46990.12
129IL_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)
130IL_90735.12
131IL_40892.12
132IL_33964.12
133IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
134IL_11751.12
135IL_90057.12
136IL_98566.12
137IL_12211.12
138IL_15840.22Triple Sheared with unpaired, inserted A
139IL_65137.12Kink-turn like motif in Group I Intron
140IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
141IL_23262.42
142IL_69536.12LSU Helix 96 (H96) IL2
143IL_94744.12Sarcin-ricin motif with extra cWW GA pair
144IL_23414.12
145IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
146IL_40845.11
147IL_25307.11
148IL_11302.11
149IL_89794.11
150IL_28644.11
151IL_52509.11
152IL_75415.11Pseudo-knot forming internal loop
153IL_88119.11
154IL_98924.11
155IL_59529.11
156IL_91904.11
157IL_21421.11
158IL_85510.11
159IL_21077.11
160IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
161IL_41153.11
162IL_03110.11
163IL_02835.11
164IL_76263.11
165IL_66744.11SSU Helix 21 (h21) IL2 E.coli
166IL_53988.11
167IL_61730.11
168IL_71685.11Sarcin-like with an intercalated basepair
169IL_25181.11
170IL_09491.11
171IL_58454.11
172IL_88367.11
173IL_49527.11
174IL_30067.11
175IL_50911.1116S h34 ILa : Part of larger motif
176IL_80714.11
177IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
178IL_41791.11
179IL_68827.11Reverse Kink-Turn
180IL_83920.11
181IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
182IL_11778.11
183IL_91078.11
184IL_06306.11
185IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
186IL_23639.11tWH-tHS-L-cWW
187IL_02957.11
188IL_18675.11cWW-bulge-cWW
189IL_40527.11Kink-turn
190IL_49976.11
191IL_52610.11
192IL_85805.11
193IL_57977.11
194IL_39324.11
195IL_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.
196IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
197IL_06421.11Single sheared with bulged bases
198IL_20775.11tSH-inserted
199IL_83856.11
200IL_76486.11Sarcin-ricin motif with syn G
201IL_70299.11
202IL_57364.11LSU Helix 89 (H89) IL2
203IL_41139.11
204IL_91044.11
205IL_87394.11
206IL_05513.11
207IL_83250.1116S h40 3WJ T.th.
208IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
209IL_06468.1116S h40 3WJ E.c.
210IL_52958.11
211IL_06808.11Double sheared (tSH-tSH) one bulged base.
212IL_71942.11
213IL_86336.11
214IL_81398.11
215IL_97842.11
216IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
217IL_64589.11
218IL_54470.11tHS tHH bulge with S-turn
219IL_06847.11Group II Intron IL
220IL_42891.11
221IL_78513.11
222IL_63952.11
223IL_86059.11
224IL_43316.11
225IL_12507.11
226IL_69799.11
227IL_47687.11
228IL_80652.11
229IL_54450.11
230IL_37347.11
231IL_46306.11
232IL_82601.11Tandem cWW water-inserted CU pairs
233IL_91089.11
234IL_60649.11Kink-turn
235IL_47732.11
236IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
237IL_80505.11
238IL_22909.11
239IL_55649.11
240IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
241IL_31224.1123S H91 IL
242IL_05221.11
243IL_06471.11
244IL_68767.11
245IL_17603.11
246IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
247IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
248IL_77296.11
249IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
250IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
251IL_06177.11cWW AG or UU
252IL_82650.11
253IL_26868.11
254IL_25082.11
255IL_53323.11
256IL_26971.11
257IL_56513.11
258IL_15205.11
259IL_87523.11
260IL_03282.11
261IL_46721.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.112481-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.11219cWW AG or water inserted cWW Y-Y.

Removed motif groups

#Motif idInstancesDescription
1IL_12024.12
2IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_03741.11

Added motif groups

#Motif idInstancesDescription
1IL_12147.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
2IL_17066.11
3IL_27640.11
4IL_37325.11
5IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)