Changes in PDB files used for clustering

Release 1.12 has 218 PDB files, release 1.13 has 220 PDB files, 217 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_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
10IL_73276.522C-loop
11IL_93424.421tSH-inserted-tHW
12IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.31716S h21 S8 binding site
14IL_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_94430.51616S h32-h33-h34 3WJ
17IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_31555.513Tandem sheared with inserted, unpaired purine.
19IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
20IL_46648.61323S H91 IL | Single-Base Intercalation Site
21IL_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)
22IL_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
23IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
25IL_58291.410Recurrent Sub-motif found in junctions
26IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_92114.39GAAA loop receptor "platform" motif
28IL_90459.39cWW AG or UU
29IL_47444.39SRP Loop E-like motif
30IL_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.
31IL_25300.3716S h19 IL and 23S H41 IL
32IL_73000.27cHS-cWS
33IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_25230.36Bacterial 5S rRNA Loop E
35IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36IL_97057.36
37IL_77263.26Kink-turn from U4
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_53635.36LSU Helix 32 (H32) IL
40IL_08926.3623S H91 IL
41IL_13069.36LSU 3WJ H32-H33-H35A
42IL_90133.36
43IL_72158.36LSU Helix 62 (H62) IL
44IL_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)
45IL_70237.36
46IL_79083.35
47IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
48IL_02359.35
49IL_86357.35LSU Helix 61 IL2
50IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
51IL_22732.14tSH-inserted-tHS
52IL_94403.54LSU H77
53IL_42251.14
54IL_38807.34
55IL_31663.1423S H73 ILa : Part of larger Motif
56IL_09530.14Double S-turn motif
57IL_34363.24Kink-turn from 23S H42
58IL_45262.44
59IL_39526.44
60IL_28572.2416S h18 kink-turn like motif
61IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
62IL_21333.24tSH-tHW-bulge
63IL_31066.34SSU Helix 44 (h44) extension
64IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
65IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
66IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
67IL_39980.14
68IL_48918.34Kink-turn variant
69IL_01080.14
70IL_98591.34
71IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
72IL_82188.24LSU H68 IL from H.m.
73IL_79955.23SSU Helix (23) h23 IL1
74IL_80494.23LSU H58 IL2 H.m.
75IL_82563.13Thi-box riboswitch T-loop
76IL_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.
77IL_28003.13
78IL_06180.13tHS tHH bulge with S-turn
79IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
80IL_95150.63
81IL_37053.13Kink-turn from 23S H58
82IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
83IL_87065.1323S H91 IL | Single-Base Intercalation Site
84IL_30840.23
85IL_62499.73
86IL_34628.23Kink-turn
87IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
88IL_07300.23
89IL_80348.3323S H91 IL
90IL_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
91IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
92IL_16166.4323S H91 IL
93IL_98421.43SSU Helix 12 (h12) IL
94IL_43946.13
95IL_06211.33
96IL_52173.13
97IL_05723.13
98IL_58586.23
99IL_87548.12
100IL_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)
101IL_33842.12
102IL_52940.12
103IL_09882.12
104IL_77076.12
105IL_96206.32
106IL_46435.12
107IL_09587.12
108IL_00998.12
109IL_23414.12
110IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
111IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
112IL_11751.12
113IL_90057.12
114IL_46034.32
115IL_65137.12Kink-turn like motif in Group I Intron
116IL_98566.12
117IL_12211.12
118IL_21495.12
119IL_67887.12
120IL_21639.12
121IL_31707.12Vitamin B12 aptamer
122IL_97833.12
123IL_15840.22Triple Sheared with unpaired, inserted A
124IL_37406.12
125IL_37197.12
126IL_76095.32Motif from Hairpin Ribozyme
127IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
128IL_97509.12Double sheared with wobble cWW.
129IL_45794.12
130IL_96446.12
131IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
132IL_23262.42
133IL_69536.12LSU Helix 96 (H96) IL2
134IL_94744.12Sarcin-ricin motif with extra cWW GA pair
135IL_16330.12
136IL_87507.12tHS tHH bulge with S-turn
137IL_50521.12
138IL_80093.12
139IL_30381.12tHS tHH bulge with S-turn
140IL_31039.12
141IL_46990.12
142IL_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)
143IL_90735.12
144IL_40892.12
145IL_33964.12
146IL_70401.12
147IL_83250.1116S h40 3WJ T.th.
148IL_57977.11
149IL_39324.11
150IL_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.
151IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
152IL_83920.11
153IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
154IL_53988.11
155IL_31224.1123S H91 IL
156IL_05221.11
157IL_06471.11
158IL_68767.11
159IL_17603.11
160IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
161IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
162IL_60649.11Kink-turn
163IL_52610.11
164IL_63952.11
165IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
166IL_11778.11
167IL_61730.11
168IL_25082.11
169IL_53323.11
170IL_26971.11
171IL_56513.11
172IL_15205.11
173IL_87523.11
174IL_77296.11
175IL_87394.11
176IL_05513.11
177IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
178IL_86059.11
179IL_43316.11
180IL_12507.11
181IL_06468.1116S h40 3WJ E.c.
182IL_06421.11Single sheared with bulged bases
183IL_20775.11tSH-inserted
184IL_75415.11Pseudo-knot forming internal loop
185IL_88119.11
186IL_98924.11
187IL_59529.11
188IL_91904.11
189IL_21421.11
190IL_85510.11
191IL_21077.11
192IL_03282.11
193IL_42891.11
194IL_78513.11
195IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
196IL_80505.11
197IL_69799.11
198IL_47687.11
199IL_52958.11
200IL_06808.11Double sheared (tSH-tSH) one bulged base.
201IL_71685.11Sarcin-like with an intercalated basepair
202IL_25181.11
203IL_09491.11
204IL_58454.11
205IL_88367.11
206IL_49527.11
207IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
208IL_47732.11
209IL_40845.11
210IL_06177.11cWW AG or UU
211IL_82650.11
212IL_22909.11
213IL_80652.11
214IL_54450.11
215IL_77014.11
216IL_91078.11
217IL_06306.11
218IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
219IL_23639.11tWH-tHS-L-cWW
220IL_02957.11
221IL_18675.11cWW-bulge-cWW
222IL_40527.11Kink-turn
223IL_49976.11
224IL_57285.11
225IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
226IL_88865.11
227IL_25307.11
228IL_26868.11
229IL_31006.11tSH-tHW-L-bif-cWW
230IL_55649.11
231IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
232IL_71942.11
233IL_83856.11
234IL_76486.11Sarcin-ricin motif with syn G
235IL_70299.11
236IL_57364.11LSU Helix 89 (H89) IL2
237IL_41139.11
238IL_23448.11
239IL_46721.11
240IL_50911.1116S h34 ILa : Part of larger motif
241IL_80714.11
242IL_03110.11
243IL_02835.11
244IL_76263.11
245IL_91379.11
246IL_11302.11
247IL_75328.11
248IL_86336.11
249IL_81398.11
250IL_97842.11
251IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
252IL_64589.11
253IL_54470.11tHS tHH bulge with S-turn
254IL_91044.11
255IL_27668.11
256IL_41153.11
257IL_85805.11
258IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
259IL_41791.11
260IL_68827.11Reverse Kink-Turn
261IL_66744.11SSU Helix 21 (h21) IL2 E.coli
262IL_89794.11
263IL_28644.11
264IL_52509.11
265IL_27243.11
266IL_37347.11
267IL_46306.11
268IL_82601.11Tandem cWW water-inserted CU pairs
269IL_91089.11
270IL_06847.11Group II Intron IL
271IL_30067.11

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_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_17066.11
4IL_27640.11
5IL_37325.11