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_77263.26Kink-turn from U4
35IL_53635.36LSU Helix 32 (H32) IL
36IL_90133.36
37IL_72158.36LSU Helix 62 (H62) IL
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_13069.36LSU 3WJ H32-H33-H35A
40IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
41IL_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)
42IL_79083.35
43IL_86357.35LSU Helix 61 IL2
44IL_02359.35
45IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
46IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
47IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
48IL_38807.34
49IL_45262.44
50IL_28572.2416S h18 kink-turn like motif
51IL_31066.34SSU Helix 44 (h44) extension
52IL_34363.24Kink-turn from 23S H42
53IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
54IL_94403.54LSU H77
55IL_42251.14
56IL_09530.14Double S-turn motif
57IL_01080.14
58IL_39526.44
59IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
61IL_98591.34
62IL_22732.14tSH-inserted-tHS
63IL_39980.14
64IL_82188.24LSU H68 IL from H.m.
65IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
66IL_21333.24tSH-tHW-bulge
67IL_48918.34Kink-turn variant
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_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.
73IL_34628.23Kink-turn
74IL_82563.13Thi-box riboswitch T-loop
75IL_87065.1323S H91 IL | Single-Base Intercalation Site
76IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
77IL_52173.13
78IL_98421.43SSU Helix 12 (h12) IL
79IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
80IL_28003.13
81IL_06180.13tHS tHH bulge with S-turn
82IL_30840.23
83IL_79955.23SSU Helix (23) h23 IL1
84IL_05723.13
85IL_07300.23
86IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
87IL_16166.4323S H91 IL
88IL_80494.23LSU H58 IL2 H.m.
89IL_62499.73
90IL_37053.13Kink-turn from 23S H58
91IL_76095.32Motif from Hairpin Ribozyme
92IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
93IL_40892.12
94IL_33964.12
95IL_30381.12tHS tHH bulge with S-turn
96IL_00998.12
97IL_97509.12Double sheared with wobble cWW.
98IL_90735.12
99IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
100IL_98566.12
101IL_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)
102IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
103IL_77076.12
104IL_09587.12
105IL_70401.12
106IL_31707.12Vitamin B12 aptamer
107IL_90057.12
108IL_46435.12
109IL_21495.12
110IL_37406.12
111IL_23414.12
112IL_33842.12
113IL_50521.12
114IL_09882.12
115IL_80093.12
116IL_21639.12
117IL_37197.12
118IL_87548.12
119IL_52940.12
120IL_12211.12
121IL_15840.22Triple Sheared with unpaired, inserted A
122IL_23262.42
123IL_69536.12LSU Helix 96 (H96) IL2
124IL_94744.12Sarcin-ricin motif with extra cWW GA pair
125IL_67887.12
126IL_45794.12
127IL_11751.12
128IL_65137.12Kink-turn like motif in Group I Intron
129IL_97833.12
130IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
131IL_16330.12
132IL_87507.12tHS tHH bulge with S-turn
133IL_39324.11
134IL_86059.11
135IL_25307.11
136IL_11302.11
137IL_53988.11
138IL_91078.11
139IL_81398.11
140IL_97842.11
141IL_46306.11
142IL_82601.11Tandem cWW water-inserted CU pairs
143IL_91089.11
144IL_60649.11Kink-turn
145IL_47732.11
146IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
147IL_40845.11
148IL_57977.11
149IL_76263.11
150IL_66744.11SSU Helix 21 (h21) IL2 E.coli
151IL_11778.11
152IL_37347.11
153IL_06471.11
154IL_68767.11
155IL_17603.11
156IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
157IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
158IL_77296.11
159IL_46721.11
160IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
161IL_68827.11Reverse Kink-Turn
162IL_83920.11
163IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
164IL_06421.11Single sheared with bulged bases
165IL_20775.11tSH-inserted
166IL_71942.11
167IL_31224.1123S H91 IL
168IL_05221.11
169IL_26971.11
170IL_56513.11
171IL_15205.11
172IL_87523.11
173IL_03282.11
174IL_41153.11
175IL_50911.1116S h34 ILa : Part of larger motif
176IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
177IL_52958.11
178IL_06808.11Double sheared (tSH-tSH) one bulged base.
179IL_25082.11
180IL_53323.11
181IL_59529.11
182IL_91904.11
183IL_21421.11
184IL_85510.11
185IL_21077.11
186IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
187IL_85805.11
188IL_02835.11
189IL_06468.1116S h40 3WJ E.c.
190IL_80652.11
191IL_54450.11
192IL_88119.11
193IL_98924.11
194IL_25181.11
195IL_09491.11
196IL_58454.11
197IL_88367.11
198IL_49527.11
199IL_30067.11
200IL_83250.1116S h40 3WJ T.th.
201IL_43316.11
202IL_12507.11
203IL_69799.11
204IL_47687.11
205IL_55649.11
206IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
207IL_75415.11Pseudo-knot forming internal loop
208IL_71685.11Sarcin-like with an intercalated basepair
209IL_02957.11
210IL_18675.11cWW-bulge-cWW
211IL_40527.11Kink-turn
212IL_49976.11
213IL_52610.11
214IL_05513.11
215IL_03110.11
216IL_41791.11
217IL_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.
218IL_80505.11
219IL_22909.11
220IL_06306.11
221IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
222IL_23639.11tWH-tHS-L-cWW
223IL_57364.11LSU Helix 89 (H89) IL2
224IL_41139.11
225IL_91044.11
226IL_87394.11
227IL_63952.11
228IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
229IL_06177.11cWW AG or UU
230IL_82650.11
231IL_26868.11
232IL_89794.11
233IL_28644.11
234IL_52509.11
235IL_61730.11
236IL_03741.11
237IL_83856.11
238IL_76486.11Sarcin-ricin motif with syn G
239IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
240IL_64589.11
241IL_54470.11tHS tHH bulge with S-turn
242IL_06847.11Group II Intron IL
243IL_42891.11

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