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_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_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_31555.513Tandem sheared with inserted, unpaired purine.
19IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
20IL_46648.61323S H91 IL | Single-Base Intercalation Site
21IL_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)
22IL_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
23IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
25IL_58291.410Recurrent Sub-motif found in junctions
26IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_92114.39GAAA loop receptor "platform" motif
28IL_90459.39cWW AG or UU
29IL_47444.39SRP Loop E-like motif
30IL_25300.3716S h19 IL and 23S H41 IL
31IL_73000.27cHS-cWS
32IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_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.
34IL_97057.36
35IL_77263.26Kink-turn from U4
36IL_25380.16LSU Helix 89 (H89) IL2
37IL_53635.36LSU Helix 32 (H32) IL
38IL_08926.3623S H91 IL
39IL_13069.36LSU 3WJ H32-H33-H35A
40IL_90133.36
41IL_72158.36LSU Helix 62 (H62) IL
42IL_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)
43IL_70237.36
44IL_25230.36Bacterial 5S rRNA Loop E
45IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
46IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_02359.35
48IL_86357.35LSU Helix 61 IL2
49IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
50IL_79083.35
51IL_34363.24Kink-turn from 23S H42
52IL_45262.44
53IL_39526.44
54IL_28572.2416S h18 kink-turn like motif
55IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
56IL_21333.24tSH-tHW-bulge
57IL_31066.34SSU Helix 44 (h44) extension
58IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
59IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
61IL_39980.14
62IL_48918.34Kink-turn variant
63IL_01080.14
64IL_98591.34
65IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
66IL_82188.24LSU H68 IL from H.m.
67IL_22732.14tSH-inserted-tHS
68IL_94403.54LSU H77
69IL_42251.14
70IL_38807.34
71IL_31663.1423S H73 ILa : Part of larger Motif
72IL_09530.14Double S-turn motif
73IL_62499.73
74IL_34628.23Kink-turn
75IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
76IL_07300.23
77IL_80348.3323S H91 IL
78IL_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
79IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
80IL_16166.4323S H91 IL
81IL_98421.43SSU Helix 12 (h12) IL
82IL_43946.13
83IL_06211.33
84IL_52173.13
85IL_05723.13
86IL_58586.23
87IL_79955.23SSU Helix (23) h23 IL1
88IL_80494.23LSU H58 IL2 H.m.
89IL_82563.13Thi-box riboswitch T-loop
90IL_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.
91IL_28003.13
92IL_06180.13tHS tHH bulge with S-turn
93IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
94IL_95150.63
95IL_37053.13Kink-turn from 23S H58
96IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
97IL_87065.1323S H91 IL | Single-Base Intercalation Site
98IL_30840.23
99IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
100IL_11751.12
101IL_90057.12
102IL_46034.32
103IL_65137.12Kink-turn like motif in Group I Intron
104IL_98566.12
105IL_12211.12
106IL_21495.12
107IL_67887.12
108IL_21639.12
109IL_31707.12Vitamin B12 aptamer
110IL_97833.12
111IL_15840.22Triple Sheared with unpaired, inserted A
112IL_37406.12
113IL_37197.12
114IL_76095.32Motif from Hairpin Ribozyme
115IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
116IL_97509.12Double sheared with wobble cWW.
117IL_45794.12
118IL_96446.12
119IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
120IL_23262.42
121IL_69536.12LSU Helix 96 (H96) IL2
122IL_94744.12Sarcin-ricin motif with extra cWW GA pair
123IL_16330.12
124IL_87507.12tHS tHH bulge with S-turn
125IL_50521.12
126IL_80093.12
127IL_30381.12tHS tHH bulge with S-turn
128IL_31039.12
129IL_46990.12
130IL_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)
131IL_90735.12
132IL_40892.12
133IL_33964.12
134IL_70401.12
135IL_87548.12
136IL_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)
137IL_33842.12
138IL_52940.12
139IL_09882.12
140IL_77076.12
141IL_96206.32
142IL_46435.12
143IL_09587.12
144IL_00998.12
145IL_23414.12
146IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
147IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
148IL_86059.11
149IL_43316.11
150IL_12507.11
151IL_06468.1116S h40 3WJ E.c.
152IL_06421.11Single sheared with bulged bases
153IL_20775.11tSH-inserted
154IL_75415.11Pseudo-knot forming internal loop
155IL_88119.11
156IL_98924.11
157IL_59529.11
158IL_91904.11
159IL_21421.11
160IL_85510.11
161IL_21077.11
162IL_03282.11
163IL_42891.11
164IL_78513.11
165IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
166IL_80505.11
167IL_69799.11
168IL_47687.11
169IL_52958.11
170IL_06808.11Double sheared (tSH-tSH) one bulged base.
171IL_71685.11Sarcin-like with an intercalated basepair
172IL_25181.11
173IL_09491.11
174IL_58454.11
175IL_88367.11
176IL_49527.11
177IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
178IL_47732.11
179IL_40845.11
180IL_06177.11cWW AG or UU
181IL_82650.11
182IL_22909.11
183IL_80652.11
184IL_54450.11
185IL_77014.11
186IL_91078.11
187IL_06306.11
188IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
189IL_23639.11tWH-tHS-L-cWW
190IL_02957.11
191IL_18675.11cWW-bulge-cWW
192IL_40527.11Kink-turn
193IL_49976.11
194IL_57285.11
195IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
196IL_88865.11
197IL_25307.11
198IL_26868.11
199IL_31006.11tSH-tHW-L-bif-cWW
200IL_55649.11
201IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
202IL_71942.11
203IL_83856.11
204IL_76486.11Sarcin-ricin motif with syn G
205IL_70299.11
206IL_57364.11LSU Helix 89 (H89) IL2
207IL_41139.11
208IL_23448.11
209IL_46721.11
210IL_50911.1116S h34 ILa : Part of larger motif
211IL_80714.11
212IL_03110.11
213IL_02835.11
214IL_76263.11
215IL_91379.11
216IL_11302.11
217IL_75328.11
218IL_86336.11
219IL_81398.11
220IL_97842.11
221IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
222IL_64589.11
223IL_54470.11tHS tHH bulge with S-turn
224IL_91044.11
225IL_27668.11
226IL_41153.11
227IL_85805.11
228IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
229IL_41791.11
230IL_68827.11Reverse Kink-Turn
231IL_66744.11SSU Helix 21 (h21) IL2 E.coli
232IL_89794.11
233IL_28644.11
234IL_52509.11
235IL_27243.11
236IL_37347.11
237IL_46306.11
238IL_82601.11Tandem cWW water-inserted CU pairs
239IL_91089.11
240IL_06847.11Group II Intron IL
241IL_30067.11
242IL_83250.1116S h40 3WJ T.th.
243IL_57977.11
244IL_39324.11
245IL_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.
246IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
247IL_83920.11
248IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
249IL_53988.11
250IL_31224.1123S H91 IL
251IL_05221.11
252IL_06471.11
253IL_68767.11
254IL_17603.11
255IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
256IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
257IL_60649.11Kink-turn
258IL_52610.11
259IL_63952.11
260IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
261IL_11778.11
262IL_61730.11
263IL_25082.11
264IL_53323.11
265IL_26971.11
266IL_56513.11
267IL_15205.11
268IL_87523.11
269IL_77296.11
270IL_87394.11
271IL_05513.11

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_12024.12
2IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_17066.11
3IL_27640.11
4IL_37325.11
5IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)