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_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_58291.410Recurrent Sub-motif found in junctions
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_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.
28IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
29IL_73000.27cHS-cWS
30IL_25230.36Bacterial 5S rRNA Loop E
31IL_70237.36
32IL_97057.36
33IL_08926.3623S H91 IL
34IL_25380.16LSU Helix 89 (H89) IL2
35IL_77263.26Kink-turn from U4
36IL_53635.36LSU Helix 32 (H32) IL
37IL_90133.36
38IL_72158.36LSU Helix 62 (H62) IL
39IL_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)
40IL_13069.36LSU 3WJ H32-H33-H35A
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_02359.35
43IL_86357.35LSU Helix 61 IL2
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_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
48IL_38807.34
49IL_45262.44
50IL_09530.14Double S-turn motif
51IL_28572.2416S h18 kink-turn like motif
52IL_31066.34SSU Helix 44 (h44) extension
53IL_34363.24Kink-turn from 23S H42
54IL_39526.44
55IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
56IL_94403.54LSU H77
57IL_42251.14
58IL_01080.14
59IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
60IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62IL_98591.34
63IL_48918.34Kink-turn variant
64IL_22732.14tSH-inserted-tHS
65IL_39980.14
66IL_82188.24LSU H68 IL from H.m.
67IL_21333.24tSH-tHW-bulge
68IL_31663.1423S H73 ILa : Part of larger Motif
69IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
70IL_58586.23
71IL_43946.13
72IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
73IL_28003.13
74IL_06180.13tHS tHH bulge with S-turn
75IL_52173.13
76IL_30840.23
77IL_98421.43SSU Helix 12 (h12) IL
78IL_07300.23
79IL_79955.23SSU Helix (23) h23 IL1
80IL_05723.13
81IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
82IL_16166.4323S H91 IL
83IL_80494.23LSU H58 IL2 H.m.
84IL_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.
85IL_34628.23Kink-turn
86IL_62499.73
87IL_37053.13Kink-turn from 23S H58
88IL_82563.13Thi-box riboswitch T-loop
89IL_87065.1323S H91 IL | Single-Base Intercalation Site
90IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
91IL_76095.32Motif from Hairpin Ribozyme
92IL_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)
93IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
94IL_33842.12
95IL_09587.12
96IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
97IL_98566.12
98IL_46435.12
99IL_21495.12
100IL_37406.12
101IL_23414.12
102IL_77076.12
103IL_21639.12
104IL_37197.12
105IL_31707.12Vitamin B12 aptamer
106IL_90057.12
107IL_15840.22Triple Sheared with unpaired, inserted A
108IL_23262.42
109IL_69536.12LSU Helix 96 (H96) IL2
110IL_94744.12Sarcin-ricin motif with extra cWW GA pair
111IL_67887.12
112IL_45794.12
113IL_50521.12
114IL_09882.12
115IL_80093.12
116IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
117IL_16330.12
118IL_87507.12tHS tHH bulge with S-turn
119IL_87548.12
120IL_52940.12
121IL_12211.12
122IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
123IL_40892.12
124IL_33964.12
125IL_11751.12
126IL_65137.12Kink-turn like motif in Group I Intron
127IL_97833.12
128IL_30381.12tHS tHH bulge with S-turn
129IL_00998.12
130IL_97509.12Double sheared with wobble cWW.
131IL_90735.12
132IL_70401.12
133IL_39324.11
134IL_86059.11
135IL_83920.11
136IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
137IL_06421.11Single sheared with bulged bases
138IL_20775.11tSH-inserted
139IL_71942.11
140IL_31224.1123S H91 IL
141IL_05221.11
142IL_26971.11
143IL_56513.11
144IL_15205.11
145IL_87523.11
146IL_03282.11
147IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
148IL_40845.11
149IL_57977.11
150IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
151IL_52958.11
152IL_06808.11Double sheared (tSH-tSH) one bulged base.
153IL_25082.11
154IL_53323.11
155IL_59529.11
156IL_91904.11
157IL_21421.11
158IL_85510.11
159IL_21077.11
160IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
161IL_05513.11
162IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
163IL_06468.1116S h40 3WJ E.c.
164IL_80652.11
165IL_54450.11
166IL_88119.11
167IL_98924.11
168IL_25181.11
169IL_09491.11
170IL_58454.11
171IL_88367.11
172IL_49527.11
173IL_30067.11
174IL_50911.1116S h34 ILa : Part of larger motif
175IL_12507.11
176IL_69799.11
177IL_47687.11
178IL_55649.11
179IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
180IL_75415.11Pseudo-knot forming internal loop
181IL_71685.11Sarcin-like with an intercalated basepair
182IL_02957.11
183IL_18675.11cWW-bulge-cWW
184IL_40527.11Kink-turn
185IL_49976.11
186IL_52610.11
187IL_85805.11
188IL_02835.11
189IL_80505.11
190IL_22909.11
191IL_06306.11
192IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
193IL_23639.11tWH-tHS-L-cWW
194IL_57364.11LSU Helix 89 (H89) IL2
195IL_41139.11
196IL_91044.11
197IL_47732.11
198IL_83250.1116S h40 3WJ T.th.
199IL_43316.11
200IL_82650.11
201IL_26868.11
202IL_89794.11
203IL_28644.11
204IL_52509.11
205IL_61730.11
206IL_03741.11
207IL_83856.11
208IL_76486.11Sarcin-ricin motif with syn G
209IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
210IL_64589.11
211IL_54470.11tHS tHH bulge with S-turn
212IL_06847.11Group II Intron IL
213IL_46721.11
214IL_03110.11
215IL_41791.11
216IL_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.
217IL_25307.11
218IL_11302.11
219IL_53988.11
220IL_91078.11
221IL_81398.11
222IL_97842.11
223IL_46306.11
224IL_82601.11Tandem cWW water-inserted CU pairs
225IL_91089.11
226IL_60649.11Kink-turn
227IL_41153.11
228IL_63952.11
229IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
230IL_06177.11cWW AG or UU
231IL_66744.11SSU Helix 21 (h21) IL2 E.coli
232IL_11778.11
233IL_37347.11
234IL_06471.11
235IL_68767.11
236IL_17603.11
237IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
238IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
239IL_77296.11

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_80348.3323S H91 IL
8IL_06211.33
9IL_95150.63
10IL_96206.32
11IL_46034.32

Removed motif groups

#Motif idInstancesDescription
1IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_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)
4IL_22358.12
5IL_95884.12
6IL_31473.12
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_46990.12
3IL_12024.12
4IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5IL_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)
6IL_31039.12
7IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
8IL_70299.11
9IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
10IL_78513.11
11IL_80714.11
12IL_86336.11