Changes in PDB files used for clustering

Release 1.11 has 213 PDB files, release 1.12 has 217 PDB files, 213 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_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_46648.61323S H91 IL | Single-Base Intercalation Site
18IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19IL_31555.513Tandem sheared with inserted, unpaired purine.
20IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
21IL_58291.410Recurrent Sub-motif found in junctions
22IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
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_47444.39SRP Loop E-like motif
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_70237.36
31IL_97057.36
32IL_08926.3623S H91 IL
33IL_77263.26Kink-turn from U4
34IL_53635.36LSU Helix 32 (H32) IL
35IL_90133.36
36IL_72158.36LSU Helix 62 (H62) IL
37IL_25380.16LSU Helix 89 (H89) IL2
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
40IL_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)
41IL_25230.36Bacterial 5S rRNA Loop E
42IL_86357.35LSU Helix 61 IL2
43IL_02359.35
44IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
46IL_79083.35
47IL_28572.2416S h18 kink-turn like motif
48IL_31066.34SSU Helix 44 (h44) extension
49IL_34363.24Kink-turn from 23S H42
50IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
51IL_94403.54LSU H77
52IL_42251.14
53IL_09530.14Double S-turn motif
54IL_01080.14
55IL_39526.44
56IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
57IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
58IL_98591.34
59IL_22732.14tSH-inserted-tHS
60IL_39980.14
61IL_82188.24LSU H68 IL from H.m.
62IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
63IL_21333.24tSH-tHW-bulge
64IL_48918.34Kink-turn variant
65IL_31663.1423S H73 ILa : Part of larger Motif
66IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
67IL_38807.34
68IL_45262.44
69IL_82563.13Thi-box riboswitch T-loop
70IL_87065.1323S H91 IL | Single-Base Intercalation Site
71IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
72IL_52173.13
73IL_98421.43SSU Helix 12 (h12) IL
74IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
75IL_28003.13
76IL_06180.13tHS tHH bulge with S-turn
77IL_30840.23
78IL_79955.23SSU Helix (23) h23 IL1
79IL_05723.13
80IL_07300.23
81IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
82IL_16166.4323S H91 IL
83IL_80494.23LSU H58 IL2 H.m.
84IL_62499.73
85IL_37053.13Kink-turn from 23S H58
86IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
87IL_58586.23
88IL_43946.13
89IL_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.
90IL_34628.23Kink-turn
91IL_30381.12tHS tHH bulge with S-turn
92IL_00998.12
93IL_97509.12Double sheared with wobble cWW.
94IL_90735.12
95IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
96IL_98566.12
97IL_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)
98IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
99IL_77076.12
100IL_09587.12
101IL_70401.12
102IL_31707.12Vitamin B12 aptamer
103IL_90057.12
104IL_46435.12
105IL_21495.12
106IL_37406.12
107IL_23414.12
108IL_33842.12
109IL_50521.12
110IL_09882.12
111IL_80093.12
112IL_21639.12
113IL_37197.12
114IL_87548.12
115IL_52940.12
116IL_12211.12
117IL_15840.22Triple Sheared with unpaired, inserted A
118IL_23262.42
119IL_69536.12LSU Helix 96 (H96) IL2
120IL_94744.12Sarcin-ricin motif with extra cWW GA pair
121IL_67887.12
122IL_45794.12
123IL_11751.12
124IL_65137.12Kink-turn like motif in Group I Intron
125IL_97833.12
126IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
127IL_16330.12
128IL_87507.12tHS tHH bulge with S-turn
129IL_76095.32Motif from Hairpin Ribozyme
130IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
131IL_40892.12
132IL_33964.12
133IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
134IL_40845.11
135IL_57977.11
136IL_76263.11
137IL_66744.11SSU Helix 21 (h21) IL2 E.coli
138IL_11778.11
139IL_37347.11
140IL_06471.11
141IL_68767.11
142IL_17603.11
143IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
144IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
145IL_77296.11
146IL_46721.11
147IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
148IL_68827.11Reverse Kink-Turn
149IL_83920.11
150IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
151IL_06421.11Single sheared with bulged bases
152IL_20775.11tSH-inserted
153IL_71942.11
154IL_31224.1123S H91 IL
155IL_05221.11
156IL_26971.11
157IL_56513.11
158IL_15205.11
159IL_87523.11
160IL_03282.11
161IL_41153.11
162IL_50911.1116S h34 ILa : Part of larger motif
163IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
164IL_52958.11
165IL_06808.11Double sheared (tSH-tSH) one bulged base.
166IL_25082.11
167IL_53323.11
168IL_59529.11
169IL_91904.11
170IL_21421.11
171IL_85510.11
172IL_21077.11
173IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
174IL_85805.11
175IL_02835.11
176IL_06468.1116S h40 3WJ E.c.
177IL_80652.11
178IL_54450.11
179IL_88119.11
180IL_98924.11
181IL_25181.11
182IL_09491.11
183IL_58454.11
184IL_88367.11
185IL_49527.11
186IL_30067.11
187IL_83250.1116S h40 3WJ T.th.
188IL_43316.11
189IL_12507.11
190IL_69799.11
191IL_47687.11
192IL_55649.11
193IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
194IL_75415.11Pseudo-knot forming internal loop
195IL_71685.11Sarcin-like with an intercalated basepair
196IL_02957.11
197IL_18675.11cWW-bulge-cWW
198IL_40527.11Kink-turn
199IL_49976.11
200IL_52610.11
201IL_05513.11
202IL_03110.11
203IL_41791.11
204IL_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.
205IL_80505.11
206IL_22909.11
207IL_06306.11
208IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
209IL_23639.11tWH-tHS-L-cWW
210IL_57364.11LSU Helix 89 (H89) IL2
211IL_41139.11
212IL_91044.11
213IL_87394.11
214IL_63952.11
215IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
216IL_06177.11cWW AG or UU
217IL_82650.11
218IL_26868.11
219IL_89794.11
220IL_28644.11
221IL_52509.11
222IL_61730.11
223IL_03741.11
224IL_83856.11
225IL_76486.11Sarcin-ricin motif with syn G
226IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
227IL_64589.11
228IL_54470.11tHS tHH bulge with S-turn
229IL_06847.11Group II Intron IL
230IL_42891.11
231IL_39324.11
232IL_86059.11
233IL_25307.11
234IL_11302.11
235IL_53988.11
236IL_91078.11
237IL_81398.11
238IL_97842.11
239IL_46306.11
240IL_82601.11Tandem cWW water-inserted CU pairs
241IL_91089.11
242IL_60649.11Kink-turn
243IL_47732.11

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_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
5IL_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)
6IL_25300.3716S h19 IL and 23S H41 IL
7IL_06211.33
8IL_95150.63
9IL_80348.3323S H91 IL
10IL_96206.32
11IL_46034.32

Removed motif groups

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

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_12024.12
3IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
4IL_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)
5IL_31039.12
6IL_46990.12
7IL_70299.11
8IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
9IL_78513.11
10IL_80714.11
11IL_86336.11
12IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW