Changes in PDB files used for clustering

Release 1.11 has 214 PDB files, release 1.12 has 218 PDB files, 214 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.12: 4C4W, 4J39, 4J5V, 4OO8.

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 1.11 has 275 motif groups, release 1.12 has 276 motif groups, 253 of them are identical.

11 motif groups were updated, 11 groups are present only in release 1.11, 12 groups are only in release 1.12.

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_41766.654Tandem cWW pairs (Not AU or GC)
3IL_39199.453Hoogsteen-edge Platform, Single bulged base
4IL_56465.447Single, unpaired intercalated base, consensus A
5IL_44540.443Sugar-edge, 1-base platform, consensus tHS
6IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_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
8IL_13959.426Double Sheared (tSH-tHS)
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_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_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_31555.513Tandem sheared with inserted, unpaired purine.
19IL_46648.61323S H91 IL | Single-Base Intercalation Site
20IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
21IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_58291.410Recurrent Sub-motif found in junctions
23IL_47444.39SRP Loop E-like motif
24IL_92114.39GAAA loop receptor "platform" motif
25IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
26IL_90459.39cWW AG or UU
27IL_73000.27cHS-cWS
28IL_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.
29IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
30IL_13069.36LSU 3WJ H32-H33-H35A
31IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
32IL_25380.16LSU Helix 89 (H89) IL2
33IL_25230.36Bacterial 5S rRNA Loop E
34IL_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)
35IL_70237.36
36IL_97057.36
37IL_08926.3623S H91 IL
38IL_77263.26Kink-turn from U4
39IL_53635.36LSU Helix 32 (H32) IL
40IL_90133.36
41IL_72158.36LSU Helix 62 (H62) IL
42IL_02359.35
43IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
44IL_86357.35LSU Helix 61 IL2
45IL_79083.35
46IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_22732.14tSH-inserted-tHS
48IL_98591.34
49IL_39526.44
50IL_21333.24tSH-tHW-bulge
51IL_39980.14
52IL_82188.24LSU H68 IL from H.m.
53IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
54IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
55IL_31663.1423S H73 ILa : Part of larger Motif
56IL_28572.2416S h18 kink-turn like motif
57IL_31066.34SSU Helix 44 (h44) extension
58IL_38807.34
59IL_45262.44
60IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
61IL_94403.54LSU H77
62IL_34363.24Kink-turn from 23S H42
63IL_01080.14
64IL_42251.14
65IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
66IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67IL_09530.14Double S-turn motif
68IL_48918.34Kink-turn variant
69IL_79955.23SSU Helix (23) h23 IL1
70IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
71IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
72IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
73IL_16166.4323S H91 IL
74IL_05723.13
75IL_62499.73
76IL_80494.23LSU H58 IL2 H.m.
77IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
78IL_37053.13Kink-turn from 23S H58
79IL_58586.23
80IL_43946.13
81IL_28003.13
82IL_06180.13tHS tHH bulge with S-turn
83IL_52173.13
84IL_30840.23
85IL_98421.43SSU Helix 12 (h12) IL
86IL_82563.13Thi-box riboswitch T-loop
87IL_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.
88IL_07300.23
89IL_87065.1323S H91 IL | Single-Base Intercalation Site
90IL_34628.23Kink-turn
91IL_50521.12
92IL_09882.12
93IL_46435.12
94IL_09587.12
95IL_16330.12
96IL_87507.12tHS tHH bulge with S-turn
97IL_70401.12
98IL_87548.12
99IL_52940.12
100IL_80093.12
101IL_21495.12
102IL_40892.12
103IL_33964.12
104IL_33842.12
105IL_11751.12
106IL_65137.12Kink-turn like motif in Group I Intron
107IL_97833.12
108IL_12211.12
109IL_37406.12
110IL_97509.12Double sheared with wobble cWW.
111IL_90735.12
112IL_76095.32Motif from Hairpin Ribozyme
113IL_15840.22Triple Sheared with unpaired, inserted A
114IL_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)
115IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
116IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
117IL_23262.42
118IL_69536.12LSU Helix 96 (H96) IL2
119IL_94744.12Sarcin-ricin motif with extra cWW GA pair
120IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
121IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
122IL_23414.12
123IL_77076.12
124IL_98566.12
125IL_30381.12tHS tHH bulge with S-turn
126IL_21639.12
127IL_37197.12
128IL_31707.12Vitamin B12 aptamer
129IL_90057.12
130IL_00998.12
131IL_67887.12
132IL_45794.12
133IL_96446.12
134IL_83250.1116S h40 3WJ T.th.
135IL_02835.11
136IL_06421.11Single sheared with bulged bases
137IL_20775.11tSH-inserted
138IL_03741.11
139IL_83856.11
140IL_76486.11Sarcin-ricin motif with syn G
141IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
142IL_64589.11
143IL_54470.11tHS tHH bulge with S-turn
144IL_91044.11
145IL_27668.11
146IL_43316.11
147IL_12507.11
148IL_06468.1116S h40 3WJ E.c.
149IL_52958.11
150IL_06808.11Double sheared (tSH-tSH) one bulged base.
151IL_77014.11
152IL_91078.11
153IL_81398.11
154IL_97842.11
155IL_46306.11
156IL_82601.11Tandem cWW water-inserted CU pairs
157IL_91089.11
158IL_06847.11Group II Intron IL
159IL_30067.11
160IL_63952.11
161IL_88865.11
162IL_03110.11
163IL_41791.11
164IL_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.
165IL_80505.11
166IL_69799.11
167IL_47687.11
168IL_80652.11
169IL_54450.11
170IL_71942.11
171IL_37347.11
172IL_06471.11
173IL_68767.11
174IL_17603.11
175IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
176IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
177IL_60649.11Kink-turn
178IL_52610.11
179IL_05513.11
180IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
181IL_06177.11cWW AG or UU
182IL_82650.11
183IL_22909.11
184IL_31006.11tSH-tHW-L-bif-cWW
185IL_55649.11
186IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
187IL_75328.11
188IL_31224.1123S H91 IL
189IL_05221.11
190IL_26971.11
191IL_56513.11
192IL_15205.11
193IL_87523.11
194IL_77296.11
195IL_87394.11
196IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
197IL_40845.11
198IL_39324.11
199IL_86059.11
200IL_25307.11
201IL_26868.11
202IL_25082.11
203IL_53323.11
204IL_59529.11
205IL_91904.11
206IL_21421.11
207IL_85510.11
208IL_21077.11
209IL_03282.11
210IL_42891.11
211IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
212IL_57977.11
213IL_76263.11
214IL_91379.11
215IL_11302.11
216IL_89794.11
217IL_28644.11
218IL_52509.11
219IL_27243.11
220IL_88119.11
221IL_98924.11
222IL_25181.11
223IL_09491.11
224IL_58454.11
225IL_88367.11
226IL_49527.11
227IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
228IL_47732.11
229IL_50911.1116S h34 ILa : Part of larger motif
230IL_68827.11Reverse Kink-Turn
231IL_66744.11SSU Helix 21 (h21) IL2 E.coli
232IL_53988.11
233IL_61730.11
234IL_75415.11Pseudo-knot forming internal loop
235IL_71685.11Sarcin-like with an intercalated basepair
236IL_02957.11
237IL_18675.11cWW-bulge-cWW
238IL_40527.11Kink-turn
239IL_49976.11
240IL_57285.11
241IL_46721.11
242IL_85805.11
243IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
244IL_83920.11
245IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
246IL_11778.11
247IL_06306.11
248IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
249IL_23639.11tWH-tHS-L-cWW
250IL_57364.11LSU Helix 89 (H89) IL2
251IL_41139.11
252IL_23448.11
253IL_41153.11

Updated motif groups

#Motif idInstancesDescription
1IL_47174.10214cWW AG or water inserted cWW Y-Y.
2IL_65553.823Kink-turn
3IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
4IL_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)
5IL_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
6IL_25300.3716S h19 IL and 23S H41 IL
7IL_80348.3323S H91 IL
8IL_06211.33
9IL_95150.63
10IL_96206.32
11IL_46034.32

Removed motif groups

#Motif idInstancesDescription
1IL_31473.12
2IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
4IL_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)
5IL_22358.12
6IL_95884.12
7IL_30354.11
8IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
9IL_34076.11
10IL_91956.11
11IL_27503.11

Added motif groups

#Motif idInstancesDescription
1IL_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
2IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_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)
4IL_31039.12
5IL_46990.12
6IL_12024.12
7IL_80714.11
8IL_86336.11
9IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
10IL_70299.11
11IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
12IL_78513.11