Changes in PDB files used for clustering

Release 1.9 has 210 PDB files, release 1.10 has 214 PDB files, 210 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.10: 3WBM, 4M30, 4M4O, 4M6D.

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 1.9 has 271 motif groups, release 1.10 has 275 motif groups, 255 of them are identical.

6 motif groups were updated, 10 groups are present only in release 1.9, 14 groups are only in release 1.10.

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_39199.453Hoogsteen-edge Platform, Single bulged base
2IL_44540.443Sugar-edge, 1-base platform, consensus tHS
3IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
4IL_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
5IL_13959.426Double Sheared (tSH-tHS)
6IL_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
7IL_65553.722Kink-turn
8IL_73276.522C-loop
9IL_93424.421tSH-inserted-tHW
10IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
11IL_92027.31716S h21 S8 binding site
12IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
13IL_94430.51616S h32-h33-h34 3WJ
14IL_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
16IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
17IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
18IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
19IL_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
20IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
21IL_58291.410Recurrent Sub-motif found in junctions
22IL_47444.39SRP Loop E-like motif
23IL_92114.39GAAA loop receptor "platform" motif
24IL_90459.39cWW AG or UU
25IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
26IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
27IL_73000.27cHS-cWS
28IL_25300.2616S h19 IL and 23S H41 IL
29IL_53635.36LSU Helix 32 (H32) IL
30IL_25230.36Bacterial 5S rRNA Loop E
31IL_13069.36LSU 3WJ H32-H33-H35A
32IL_90133.36
33IL_72158.36LSU Helix 62 (H62) IL
34IL_08926.3623S H91 IL
35IL_77263.26Kink-turn from U4
36IL_70237.36
37IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_97057.36
40IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
41IL_86357.35LSU Helix 61 IL2
42IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
43IL_79083.35
44IL_02359.35
45IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
46IL_21333.24tSH-tHW-bulge
47IL_28572.2416S h18 kink-turn like motif
48IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
49IL_39980.14
50IL_98591.34
51IL_31066.34SSU Helix 44 (h44) extension
52IL_82188.24LSU H68 IL from H.m.
53IL_09530.14Double S-turn motif
54IL_48918.34Kink-turn variant
55IL_01080.14
56IL_39526.44
57IL_94403.54LSU H77
58IL_38807.34
59IL_31663.1423S H73 ILa : Part of larger Motif
60IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
61IL_22732.14tSH-inserted-tHS
62IL_42251.14
63IL_34363.24Kink-turn from 23S H42
64IL_45262.44
65IL_79955.23SSU Helix (23) h23 IL1
66IL_46034.23
67IL_06180.13tHS tHH bulge with S-turn
68IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
69IL_28003.13
70IL_30840.23
71IL_62499.73
72IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
73IL_16166.4323S H91 IL
74IL_43946.13
75IL_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.
76IL_05723.13
77IL_82563.13Thi-box riboswitch T-loop
78IL_87065.1323S H91 IL | Single-Base Intercalation Site
79IL_34628.23Kink-turn
80IL_07300.23
81IL_96206.23
82IL_52173.13
83IL_98421.43SSU Helix 12 (h12) IL
84IL_58586.23
85IL_80494.23LSU H58 IL2 H.m.
86IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
87IL_37053.13Kink-turn from 23S H58
88IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
89IL_06211.23
90IL_87548.12
91IL_90057.12
92IL_98566.12
93IL_12211.12
94IL_23262.42
95IL_69536.12LSU Helix 96 (H96) IL2
96IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
97IL_52940.12
98IL_65137.12Kink-turn like motif in Group I Intron
99IL_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)
100IL_15840.22Triple Sheared with unpaired, inserted A
101IL_11751.12
102IL_97833.12
103IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
104IL_23414.12
105IL_80348.2223S H91 IL
106IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
107IL_76095.32Motif from Hairpin Ribozyme
108IL_00998.12
109IL_21639.12
110IL_37197.12
111IL_96446.12
112IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
113IL_22358.12
114IL_80093.12
115IL_30381.12tHS tHH bulge with S-turn
116IL_95150.52
117IL_67887.12
118IL_45794.12
119IL_31707.12Vitamin B12 aptamer
120IL_16330.12
121IL_87507.12tHS tHH bulge with S-turn
122IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
123IL_46435.12
124IL_09587.12
125IL_21495.12
126IL_37406.12
127IL_40892.12
128IL_33964.12
129IL_50521.12
130IL_09882.12
131IL_77076.12
132IL_94744.12Sarcin-ricin motif with extra cWW GA pair
133IL_97509.12Double sheared with wobble cWW.
134IL_90735.12
135IL_83250.1116S h40 3WJ T.th.
136IL_80505.11
137IL_69799.11
138IL_47687.11
139IL_27243.11
140IL_75328.11
141IL_31224.1123S H91 IL
142IL_05221.11
143IL_26971.11
144IL_56513.11
145IL_15205.11
146IL_21077.11
147IL_03282.11
148IL_42891.11
149IL_63952.11
150IL_06177.11cWW AG or UU
151IL_82650.11
152IL_22909.11
153IL_89794.11
154IL_28644.11
155IL_52509.11
156IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
157IL_25082.11
158IL_53323.11
159IL_59529.11
160IL_91904.11
161IL_21421.11
162IL_85510.11
163IL_49527.11
164IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
165IL_47732.11
166IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
167IL_25307.11
168IL_26868.11
169IL_53988.11
170IL_61730.11
171IL_88119.11
172IL_98924.11
173IL_25181.11
174IL_09491.11
175IL_58454.11
176IL_88367.11
177IL_49976.11
178IL_57285.11
179IL_30354.11
180IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
181IL_88865.11
182IL_02835.11
183IL_76263.11
184IL_91379.11
185IL_11302.11
186IL_11778.11
187IL_75415.11Pseudo-knot forming internal loop
188IL_71685.11Sarcin-like with an intercalated basepair
189IL_02957.11
190IL_18675.11cWW-bulge-cWW
191IL_40527.11Kink-turn
192IL_23448.11
193IL_46721.11
194IL_40845.11
195IL_03110.11
196IL_41791.11
197IL_68827.11Reverse Kink-Turn
198IL_66744.11SSU Helix 21 (h21) IL2 E.coli
199IL_06421.11Single sheared with bulged bases
200IL_20775.11tSH-inserted
201IL_06306.11
202IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
203IL_23639.11tWH-tHS-L-cWW
204IL_57364.11LSU Helix 89 (H89) IL2
205IL_41139.11
206IL_91044.11
207IL_27668.11
208IL_41153.11
209IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
210IL_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.
211IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
212IL_83920.11
213IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
214IL_52958.11
215IL_06808.11Double sheared (tSH-tSH) one bulged base.
216IL_03741.11
217IL_83856.11
218IL_76486.11Sarcin-ricin motif with syn G
219IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
220IL_64589.11
221IL_54470.11tHS tHH bulge with S-turn
222IL_06847.11Group II Intron IL
223IL_30067.11
224IL_05513.11
225IL_50911.1116S h34 ILa : Part of larger motif
226IL_57977.11
227IL_39324.11
228IL_80652.11
229IL_54450.11
230IL_77014.11
231IL_91078.11
232IL_81398.11
233IL_97842.11
234IL_46306.11
235IL_82601.11Tandem cWW water-inserted CU pairs
236IL_91089.11
237IL_60649.11Kink-turn
238IL_52610.11
239IL_85805.11
240IL_86059.11
241IL_43316.11
242IL_12507.11
243IL_06468.1116S h40 3WJ E.c.
244IL_31006.11tSH-tHW-L-bif-cWW
245IL_55649.11
246IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
247IL_71942.11
248IL_37347.11
249IL_06471.11
250IL_68767.11
251IL_17603.11
252IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
253IL_87523.11
254IL_77296.11
255IL_87394.11

Updated 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_56465.447Single, unpaired intercalated base, consensus A
5IL_31555.513Tandem sheared with inserted, unpaired purine.
6IL_46648.61323S H91 IL | Single-Base Intercalation Site

Removed motif groups

#Motif idInstancesDescription
1IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
2IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
3IL_15709.14Single 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)
4IL_75447.13
5IL_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
6IL_09520.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
7IL_19898.12
8IL_51403.12
9IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
10IL_90086.11

Added motif groups

#Motif idInstancesDescription
1IL_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.
2IL_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)
3IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
4IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
5IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
6IL_31473.12
7IL_70401.12
8IL_33842.12
9IL_95884.12
10IL_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)
11IL_27503.11
12IL_91956.11
13IL_34076.11
14IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)