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_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
10IL_73276.522C-loop
11IL_93424.421tSH-inserted-tHW
12IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.31716S h21 S8 binding site
14IL_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_94430.51616S h32-h33-h34 3WJ
16IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_46648.61323S H91 IL | Single-Base Intercalation Site
18IL_31555.513Tandem sheared with inserted, unpaired purine.
19IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
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_90459.39cWW AG or UU
24IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
25IL_47444.39SRP Loop E-like motif
26IL_92114.39GAAA loop receptor "platform" motif
27IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
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_73000.27cHS-cWS
30IL_13069.36LSU 3WJ H32-H33-H35A
31IL_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)
32IL_97057.36
33IL_70237.36
34IL_25230.36Bacterial 5S rRNA Loop E
35IL_53635.36LSU Helix 32 (H32) IL
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_08926.3623S H91 IL
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_72158.36LSU Helix 62 (H62) IL
40IL_77263.26Kink-turn from U4
41IL_90133.36
42IL_02359.35
43IL_79083.35
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_86357.35LSU Helix 61 IL2
47IL_09530.14Double S-turn motif
48IL_22732.14tSH-inserted-tHS
49IL_28572.2416S h18 kink-turn like motif
50IL_98591.34
51IL_31663.1423S H73 ILa : Part of larger Motif
52IL_39526.44
53IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
54IL_45262.44
55IL_94403.54LSU H77
56IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
57IL_39980.14
58IL_42251.14
59IL_21333.24tSH-tHW-bulge
60IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_38807.34
62IL_48918.34Kink-turn variant
63IL_01080.14
64IL_31066.34SSU Helix 44 (h44) extension
65IL_34363.24Kink-turn from 23S H42
66IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
67IL_82188.24LSU H68 IL from H.m.
68IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
69IL_28003.13
70IL_34628.23Kink-turn
71IL_43946.13
72IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
73IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
74IL_58586.23
75IL_79955.23SSU Helix (23) h23 IL1
76IL_82563.13Thi-box riboswitch T-loop
77IL_37053.13Kink-turn from 23S H58
78IL_05723.13
79IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
80IL_80494.23LSU H58 IL2 H.m.
81IL_07300.23
82IL_16166.4323S H91 IL
83IL_52173.13
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_06180.13tHS tHH bulge with S-turn
86IL_87065.1323S H91 IL | Single-Base Intercalation Site
87IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
88IL_30840.23
89IL_62499.73
90IL_98421.43SSU Helix 12 (h12) IL
91IL_21639.12
92IL_87548.12
93IL_98566.12
94IL_09587.12
95IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
96IL_65137.12Kink-turn like motif in Group I Intron
97IL_90735.12
98IL_09882.12
99IL_50521.12
100IL_70401.12
101IL_76095.32Motif from Hairpin Ribozyme
102IL_80093.12
103IL_15840.22Triple Sheared with unpaired, inserted A
104IL_23262.42
105IL_31707.12Vitamin B12 aptamer
106IL_37197.12
107IL_67887.12
108IL_11751.12
109IL_23414.12
110IL_45794.12
111IL_77076.12
112IL_97509.12Double sheared with wobble cWW.
113IL_16330.12
114IL_30381.12tHS tHH bulge with S-turn
115IL_33842.12
116IL_37406.12
117IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
118IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
119IL_94744.12Sarcin-ricin motif with extra cWW GA pair
120IL_97833.12
121IL_00998.12
122IL_12211.12
123IL_33964.12
124IL_69536.12LSU Helix 96 (H96) IL2
125IL_87507.12tHS tHH bulge with S-turn
126IL_90057.12
127IL_21495.12
128IL_40892.12
129IL_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)
130IL_46435.12
131IL_52940.12
132IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
133IL_05221.11
134IL_06468.1116S h40 3WJ E.c.
135IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
136IL_25082.11
137IL_31224.1123S H91 IL
138IL_39324.11
139IL_41139.11
140IL_49527.11
141IL_52958.11
142IL_55649.11
143IL_58454.11
144IL_64589.11
145IL_05513.11
146IL_06471.11
147IL_18675.11cWW-bulge-cWW
148IL_25181.11
149IL_41153.11
150IL_46721.11
151IL_49976.11
152IL_53323.11
153IL_75415.11Pseudo-knot forming internal loop
154IL_85805.11
155IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
156IL_02835.11
157IL_06808.11Double sheared (tSH-tSH) one bulged base.
158IL_15205.11
159IL_20775.11tSH-inserted
160IL_22909.11
161IL_28644.11
162IL_59529.11
163IL_66744.11SSU Helix 21 (h21) IL2 E.coli
164IL_82601.11Tandem cWW water-inserted CU pairs
165IL_86059.11
166IL_88119.11
167IL_91044.11
168IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
169IL_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.
170IL_06847.11Group II Intron IL
171IL_11302.11
172IL_21077.11
173IL_41791.11
174IL_47687.11
175IL_50911.1116S h34 ILa : Part of larger motif
176IL_53988.11
177IL_56513.11
178IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
179IL_71685.11Sarcin-like with an intercalated basepair
180IL_76486.11Sarcin-ricin motif with syn G
181IL_82650.11
182IL_88367.11
183IL_91078.11
184IL_98924.11
185IL_02957.11
186IL_06177.11cWW AG or UU
187IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
188IL_25307.11
189IL_30067.11
190IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
191IL_37347.11
192IL_47732.11
193IL_54450.11
194IL_57364.11LSU Helix 89 (H89) IL2
195IL_60649.11Kink-turn
196IL_68767.11
197IL_71942.11
198IL_80505.11
199IL_83250.1116S h40 3WJ T.th.
200IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
201IL_91089.11
202IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
203IL_03110.11
204IL_11778.11
205IL_23639.11tWH-tHS-L-cWW
206IL_40527.11Kink-turn
207IL_52509.11
208IL_54470.11tHS tHH bulge with S-turn
209IL_61730.11
210IL_80652.11
211IL_83856.11
212IL_89794.11
213IL_91904.11
214IL_03282.11
215IL_06306.11
216IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
217IL_21421.11
218IL_26868.11
219IL_40845.11
220IL_43316.11
221IL_46306.11
222IL_52610.11
223IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
224IL_57977.11
225IL_77296.11
226IL_81398.11
227IL_83920.11
228IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
229IL_97842.11
230IL_03741.11
231IL_06421.11Single sheared with bulged bases
232IL_09491.11
233IL_12507.11
234IL_17603.11
235IL_26971.11
236IL_63952.11
237IL_69799.11
238IL_85510.11
239IL_87523.11

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_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)
5IL_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
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_31473.12
2IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
4IL_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)
5IL_22358.12
6IL_95884.12
7IL_30354.11
8IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
9IL_34076.11
10IL_91956.11
11IL_27503.11

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_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_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)
4IL_31039.12
5IL_46990.12
6IL_12024.12
7IL_80714.11
8IL_86336.11
9IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
10IL_70299.11
11IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
12IL_78513.11