Changes in PDB files used for clustering

Release 1.12 has 218 PDB files, release 1.13 has 220 PDB files, 217 of them are identical.

1 equivalence classes changed representatives: 3SD34LVZ.

2 new structures in release 1.13: 4JK0, 4NGF.

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 1.12 has 276 motif groups, release 1.13 has 278 motif groups, 271 of them are identical.

2 motif groups were updated, 3 groups are present only in release 1.12, 5 groups are only in release 1.13.

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_41766.654Tandem cWW pairs (Not AU or GC)
2IL_39199.453Hoogsteen-edge Platform, Single bulged base
3IL_56465.447Single, unpaired intercalated base, consensus A
4IL_44540.443Sugar-edge, 1-base platform, consensus tHS
5IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
6IL_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
7IL_13959.426Double Sheared (tSH-tHS)
8IL_65553.823Kink-turn
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_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_94430.51616S h32-h33-h34 3WJ
17IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_46648.61323S H91 IL | Single-Base Intercalation Site
19IL_31555.513Tandem sheared with inserted, unpaired purine.
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
22IL_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)
23IL_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
24IL_58291.410Recurrent Sub-motif found in junctions
25IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_47444.39SRP Loop E-like motif
27IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_92114.39GAAA loop receptor "platform" motif
29IL_90459.39cWW AG or UU
30IL_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.
31IL_25300.3716S h19 IL and 23S H41 IL
32IL_73000.27cHS-cWS
33IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_70237.36
35IL_25230.36Bacterial 5S rRNA Loop E
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_97057.36
38IL_77263.26Kink-turn from U4
39IL_25380.16LSU Helix 89 (H89) IL2
40IL_53635.36LSU Helix 32 (H32) IL
41IL_08926.3623S H91 IL
42IL_13069.36LSU 3WJ H32-H33-H35A
43IL_90133.36
44IL_72158.36LSU Helix 62 (H62) IL
45IL_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)
46IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
47IL_79083.35
48IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
49IL_02359.35
50IL_86357.35LSU Helix 61 IL2
51IL_01080.14
52IL_98591.34
53IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
54IL_82188.24LSU H68 IL from H.m.
55IL_22732.14tSH-inserted-tHS
56IL_94403.54LSU H77
57IL_42251.14
58IL_38807.34
59IL_31663.1423S H73 ILa : Part of larger Motif
60IL_09530.14Double S-turn motif
61IL_34363.24Kink-turn from 23S H42
62IL_45262.44
63IL_39526.44
64IL_28572.2416S h18 kink-turn like motif
65IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
66IL_21333.24tSH-tHW-bulge
67IL_31066.34SSU Helix 44 (h44) extension
68IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
69IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
70IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
71IL_39980.14
72IL_48918.34Kink-turn variant
73IL_06211.33
74IL_52173.13
75IL_05723.13
76IL_58586.23
77IL_79955.23SSU Helix (23) h23 IL1
78IL_80494.23LSU H58 IL2 H.m.
79IL_82563.13Thi-box riboswitch T-loop
80IL_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.
81IL_28003.13
82IL_06180.13tHS tHH bulge with S-turn
83IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
84IL_95150.63
85IL_37053.13Kink-turn from 23S H58
86IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
87IL_87065.1323S H91 IL | Single-Base Intercalation Site
88IL_30840.23
89IL_62499.73
90IL_34628.23Kink-turn
91IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
92IL_07300.23
93IL_80348.3323S H91 IL
94IL_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
95IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
96IL_16166.4323S H91 IL
97IL_98421.43SSU Helix 12 (h12) IL
98IL_43946.13
99IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
100IL_23262.42
101IL_69536.12LSU Helix 96 (H96) IL2
102IL_94744.12Sarcin-ricin motif with extra cWW GA pair
103IL_16330.12
104IL_87507.12tHS tHH bulge with S-turn
105IL_50521.12
106IL_80093.12
107IL_30381.12tHS tHH bulge with S-turn
108IL_31039.12
109IL_46990.12
110IL_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)
111IL_90735.12
112IL_40892.12
113IL_33964.12
114IL_70401.12
115IL_87548.12
116IL_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)
117IL_33842.12
118IL_52940.12
119IL_09882.12
120IL_77076.12
121IL_96206.32
122IL_46435.12
123IL_09587.12
124IL_00998.12
125IL_23414.12
126IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
127IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
128IL_11751.12
129IL_90057.12
130IL_46034.32
131IL_65137.12Kink-turn like motif in Group I Intron
132IL_98566.12
133IL_12211.12
134IL_21495.12
135IL_67887.12
136IL_21639.12
137IL_31707.12Vitamin B12 aptamer
138IL_97833.12
139IL_15840.22Triple Sheared with unpaired, inserted A
140IL_37406.12
141IL_37197.12
142IL_76095.32Motif from Hairpin Ribozyme
143IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
144IL_97509.12Double sheared with wobble cWW.
145IL_45794.12
146IL_96446.12
147IL_50911.1116S h34 ILa : Part of larger motif
148IL_80714.11
149IL_03110.11
150IL_02835.11
151IL_76263.11
152IL_91379.11
153IL_11302.11
154IL_75328.11
155IL_86336.11
156IL_81398.11
157IL_97842.11
158IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
159IL_64589.11
160IL_54470.11tHS tHH bulge with S-turn
161IL_91044.11
162IL_27668.11
163IL_41153.11
164IL_85805.11
165IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
166IL_41791.11
167IL_68827.11Reverse Kink-Turn
168IL_66744.11SSU Helix 21 (h21) IL2 E.coli
169IL_89794.11
170IL_28644.11
171IL_52509.11
172IL_27243.11
173IL_37347.11
174IL_46306.11
175IL_82601.11Tandem cWW water-inserted CU pairs
176IL_91089.11
177IL_06847.11Group II Intron IL
178IL_30067.11
179IL_83250.1116S h40 3WJ T.th.
180IL_57977.11
181IL_39324.11
182IL_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.
183IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
184IL_83920.11
185IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
186IL_53988.11
187IL_31224.1123S H91 IL
188IL_05221.11
189IL_06471.11
190IL_68767.11
191IL_17603.11
192IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
193IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
194IL_60649.11Kink-turn
195IL_52610.11
196IL_63952.11
197IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
198IL_11778.11
199IL_61730.11
200IL_25082.11
201IL_53323.11
202IL_26971.11
203IL_56513.11
204IL_15205.11
205IL_87523.11
206IL_77296.11
207IL_87394.11
208IL_05513.11
209IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
210IL_86059.11
211IL_43316.11
212IL_12507.11
213IL_06468.1116S h40 3WJ E.c.
214IL_06421.11Single sheared with bulged bases
215IL_20775.11tSH-inserted
216IL_75415.11Pseudo-knot forming internal loop
217IL_88119.11
218IL_98924.11
219IL_59529.11
220IL_91904.11
221IL_21421.11
222IL_85510.11
223IL_21077.11
224IL_03282.11
225IL_42891.11
226IL_78513.11
227IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
228IL_80505.11
229IL_69799.11
230IL_47687.11
231IL_52958.11
232IL_06808.11Double sheared (tSH-tSH) one bulged base.
233IL_71685.11Sarcin-like with an intercalated basepair
234IL_25181.11
235IL_09491.11
236IL_58454.11
237IL_88367.11
238IL_49527.11
239IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
240IL_47732.11
241IL_40845.11
242IL_06177.11cWW AG or UU
243IL_82650.11
244IL_22909.11
245IL_80652.11
246IL_54450.11
247IL_77014.11
248IL_91078.11
249IL_06306.11
250IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
251IL_23639.11tWH-tHS-L-cWW
252IL_02957.11
253IL_18675.11cWW-bulge-cWW
254IL_40527.11Kink-turn
255IL_49976.11
256IL_57285.11
257IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
258IL_88865.11
259IL_25307.11
260IL_26868.11
261IL_31006.11tSH-tHW-L-bif-cWW
262IL_55649.11
263IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
264IL_71942.11
265IL_83856.11
266IL_76486.11Sarcin-ricin motif with syn G
267IL_70299.11
268IL_57364.11LSU Helix 89 (H89) IL2
269IL_41139.11
270IL_23448.11
271IL_46721.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.112481-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.11219cWW AG or water inserted cWW Y-Y.

Removed motif groups

#Motif idInstancesDescription
1IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
2IL_12024.12
3IL_03741.11

Added motif groups

#Motif idInstancesDescription
1IL_12147.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
2IL_27640.11
3IL_37325.11
4IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5IL_17066.11