Changes in PDB files used for clustering

Release 1.9 has 209 PDB files, release 1.10 has 213 PDB files, 209 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_73276.522C-loop
7IL_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
8IL_65553.722Kink-turn
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_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
18IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
23IL_47444.39SRP Loop E-like motif
24IL_90459.39cWW AG or UU
25IL_92114.39GAAA loop receptor "platform" motif
26IL_73000.27cHS-cWS
27IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28IL_70237.36
29IL_97057.36
30IL_25300.2616S h19 IL and 23S H41 IL
31IL_53635.36LSU Helix 32 (H32) IL
32IL_13069.36LSU 3WJ H32-H33-H35A
33IL_90133.36
34IL_72158.36LSU Helix 62 (H62) IL
35IL_08926.3623S H91 IL
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_25380.16LSU Helix 89 (H89) IL2
38IL_77263.26Kink-turn from U4
39IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
40IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
41IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
42IL_86357.35LSU Helix 61 IL2
43IL_79083.35
44IL_02359.35
45IL_01080.14
46IL_38807.34
47IL_31663.1423S H73 ILa : Part of larger Motif
48IL_94403.54LSU H77
49IL_42251.14
50IL_34363.24Kink-turn from 23S H42
51IL_45262.44
52IL_48918.34Kink-turn variant
53IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
54IL_22732.14tSH-inserted-tHS
55IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
56IL_21333.24tSH-tHW-bulge
57IL_39980.14
58IL_98591.34
59IL_09530.14Double S-turn motif
60IL_28572.2416S h18 kink-turn like motif
61IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
62IL_82188.24LSU H68 IL from H.m.
63IL_39526.44
64IL_31066.34SSU Helix 44 (h44) extension
65IL_98421.43SSU Helix 12 (h12) IL
66IL_37053.13Kink-turn from 23S H58
67IL_07300.23
68IL_06211.23
69IL_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.
70IL_34628.23Kink-turn
71IL_79955.23SSU Helix (23) h23 IL1
72IL_46034.23
73IL_87065.1323S H91 IL | Single-Base Intercalation Site
74IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
75IL_43946.13
76IL_82563.13Thi-box riboswitch T-loop
77IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
78IL_62499.73
79IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
80IL_16166.4323S H91 IL
81IL_05723.13
82IL_06180.13tHS tHH bulge with S-turn
83IL_28003.13
84IL_30840.23
85IL_96206.23
86IL_52173.13
87IL_58586.23
88IL_80494.23LSU H58 IL2 H.m.
89IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
90IL_31707.12Vitamin B12 aptamer
91IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
92IL_46435.12
93IL_23262.42
94IL_69536.12LSU Helix 96 (H96) IL2
95IL_21639.12
96IL_37197.12
97IL_67887.12
98IL_45794.12
99IL_50521.12
100IL_09882.12
101IL_77076.12
102IL_98566.12
103IL_12211.12
104IL_15840.22Triple Sheared with unpaired, inserted A
105IL_16330.12
106IL_87507.12tHS tHH bulge with S-turn
107IL_87548.12
108IL_90057.12
109IL_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)
110IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
111IL_00998.12
112IL_95150.52
113IL_40892.12
114IL_33964.12
115IL_52940.12
116IL_65137.12Kink-turn like motif in Group I Intron
117IL_97509.12Double sheared with wobble cWW.
118IL_90735.12
119IL_11751.12
120IL_97833.12
121IL_30381.12tHS tHH bulge with S-turn
122IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
123IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
124IL_76095.32Motif from Hairpin Ribozyme
125IL_80093.12
126IL_37406.12
127IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
128IL_22358.12
129IL_09587.12
130IL_21495.12
131IL_94744.12Sarcin-ricin motif with extra cWW GA pair
132IL_23414.12
133IL_80348.2223S H91 IL
134IL_57977.11
135IL_39324.11
136IL_06468.1116S h40 3WJ E.c.
137IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
138IL_75415.11Pseudo-knot forming internal loop
139IL_71685.11Sarcin-like with an intercalated basepair
140IL_02957.11
141IL_18675.11cWW-bulge-cWW
142IL_40527.11Kink-turn
143IL_91044.11
144IL_87394.11
145IL_50911.1116S h34 ILa : Part of larger motif
146IL_86059.11
147IL_43316.11
148IL_12507.11
149IL_69799.11
150IL_47687.11
151IL_89794.11
152IL_28644.11
153IL_52509.11
154IL_61730.11
155IL_06306.11
156IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
157IL_23639.11tWH-tHS-L-cWW
158IL_57364.11LSU Helix 89 (H89) IL2
159IL_41139.11
160IL_06847.11Group II Intron IL
161IL_42891.11
162IL_85805.11
163IL_80505.11
164IL_22909.11
165IL_53988.11
166IL_03741.11
167IL_83856.11
168IL_76486.11Sarcin-ricin motif with syn G
169IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
170IL_64589.11
171IL_54470.11tHS tHH bulge with S-turn
172IL_60649.11Kink-turn
173IL_47732.11
174IL_83250.1116S h40 3WJ T.th.
175IL_06177.11cWW AG or UU
176IL_82650.11
177IL_26868.11
178IL_11778.11
179IL_91078.11
180IL_81398.11
181IL_97842.11
182IL_46306.11
183IL_82601.11Tandem cWW water-inserted CU pairs
184IL_91089.11
185IL_77296.11
186IL_30354.11
187IL_63952.11
188IL_25307.11
189IL_11302.11
190IL_06421.11Single sheared with bulged bases
191IL_20775.11tSH-inserted
192IL_37347.11
193IL_06471.11
194IL_68767.11
195IL_17603.11
196IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
197IL_87523.11
198IL_03282.11
199IL_46721.11
200IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
201IL_02835.11
202IL_76263.11
203IL_66744.11SSU Helix 21 (h21) IL2 E.coli
204IL_52958.11
205IL_06808.11Double sheared (tSH-tSH) one bulged base.
206IL_71942.11
207IL_31224.1123S H91 IL
208IL_05221.11
209IL_26971.11
210IL_56513.11
211IL_15205.11
212IL_21077.11
213IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
214IL_41153.11
215IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
216IL_03110.11
217IL_41791.11
218IL_68827.11Reverse Kink-Turn
219IL_83920.11
220IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
221IL_80652.11
222IL_54450.11
223IL_25082.11
224IL_53323.11
225IL_59529.11
226IL_91904.11
227IL_21421.11
228IL_85510.11
229IL_49527.11
230IL_30067.11
231IL_05513.11
232IL_40845.11
233IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
234IL_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.
235IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
236IL_55649.11
237IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
238IL_88119.11
239IL_98924.11
240IL_25181.11
241IL_09491.11
242IL_58454.11
243IL_88367.11
244IL_49976.11
245IL_52610.11

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_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
5IL_75447.13
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_31473.12
6IL_70401.12
7IL_33842.12
8IL_95884.12
9IL_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)
10IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
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)