Changes in PDB files used for clustering

Release 1.6 has 203 PDB files, release 1.7 has 203 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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 1.6 has 272 motif groups, release 1.7 has 272 motif groups, 272 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.6, 0 groups are only in release 1.7.

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_97217.72431-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.8205cWW AG or water inserted cWW Y-Y.
3IL_39199.453Hoogsteen-edge Platform, Single bulged base
4IL_41766.449Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.443Sugar-edge, 1-base platform, consensus tHS
7IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_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
9IL_13959.426Double Sheared (tSH-tHS)
10IL_65553.722Kink-turn
11IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
12IL_93424.421tSH-inserted-tHW
13IL_73276.421C-loop
14IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
18IL_94430.51616S h32-h33-h34 3WJ
19IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
20IL_31555.413Tandem sheared with inserted, unpaired purine.
21IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_46648.41123S H91 IL | Single-Base Intercalation Site
23IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
25IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_58291.410Recurrent Sub-motif found in junctions
27IL_17212.110cWW 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
28IL_47444.39SRP Loop E-like motif
29IL_90459.39cWW AG or UU
30IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_92114.39GAAA loop receptor "platform" motif
32IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_73000.27cHS-cWS
35IL_70237.36
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_77263.26Kink-turn from U4
40IL_97057.36
41IL_53635.36LSU Helix 32 (H32) IL
42IL_13069.36LSU 3WJ H32-H33-H35A
43IL_90133.36
44IL_72158.36LSU Helix 62 (H62) IL
45IL_08926.3623S H91 IL
46IL_79083.35
47IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48IL_25300.1516S h19 IL and 23S H41 IL
49IL_02359.35
50IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
51IL_86357.35LSU Helix 61 IL2
52IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
53IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
54IL_22732.14tSH-inserted-tHS
55IL_98591.34
56IL_94403.34LSU H77
57IL_82188.24LSU H68 IL from H.m.
58IL_42251.14
59IL_38807.34
60IL_31663.1423S H73 ILa : Part of larger Motif
61IL_09530.14Double S-turn motif
62IL_28572.2416S h18 kink-turn like motif
63IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
64IL_21333.24tSH-tHW-bulge
65IL_34363.24Kink-turn from 23S H42
66IL_45262.44
67IL_39526.44
68IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
69IL_31066.34SSU Helix 44 (h44) extension
70IL_01080.14
71IL_39980.14
72IL_15709.14Single 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)
73IL_05723.13
74IL_43946.13
75IL_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.
76IL_34628.23Kink-turn
77IL_79955.23SSU Helix (23) h23 IL1
78IL_95150.43
79IL_75447.13
80IL_87065.1323S H91 IL | Single-Base Intercalation Site
81IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
82IL_07300.23
83IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
84IL_80494.23LSU H58 IL2 H.m.
85IL_82563.13Thi-box riboswitch T-loop
86IL_62499.73
87IL_37053.13Kink-turn from 23S H58
88IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
89IL_48918.23Kink-turn variant
90IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
91IL_80348.1323S H91 IL
92IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
93IL_16166.4323S H91 IL
94IL_06180.13tHS tHH bulge with S-turn
95IL_98421.43SSU Helix 12 (h12) IL
96IL_52173.13
97IL_30840.23
98IL_06211.13
99IL_58586.23
100IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
101IL_50521.12
102IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
103IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
104IL_46034.12
105IL_87548.12
106IL_09882.12
107IL_80093.12
108IL_30381.12tHS tHH bulge with S-turn
109IL_00998.12
110IL_21639.12
111IL_52940.12
112IL_77076.12
113IL_97509.12Double sheared with wobble cWW.
114IL_37197.12
115IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
116IL_11751.12
117IL_65137.12Kink-turn like motif in Group I Intron
118IL_19898.12
119IL_90057.12
120IL_96206.12
121IL_09587.12
122IL_80433.12
123IL_45794.12
124IL_46435.12
125IL_37406.12
126IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
127IL_16330.12
128IL_87507.12tHS tHH bulge with S-turn
129IL_31707.12Vitamin B12 aptamer
130IL_97833.12
131IL_98566.12
132IL_21495.12
133IL_94744.12Sarcin-ricin motif with extra cWW GA pair
134IL_23414.12
135IL_90735.12
136IL_40892.12
137IL_33964.12
138IL_76095.32Motif from Hairpin Ribozyme
139IL_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)
140IL_12211.12
141IL_01054.12
142IL_15840.22Triple Sheared with unpaired, inserted A
143IL_23262.42
144IL_69536.12LSU Helix 96 (H96) IL2
145IL_67887.12
146IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
147IL_85805.11
148IL_03110.11
149IL_02835.11
150IL_25307.11
151IL_11302.11
152IL_53988.11
153IL_03741.11
154IL_88119.11
155IL_98924.11
156IL_59529.11
157IL_91904.11
158IL_21421.11
159IL_85510.11
160IL_49527.11
161IL_30067.11
162IL_41153.11
163IL_83250.1116S h40 3WJ T.th.
164IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
165IL_41791.11
166IL_76263.11
167IL_66744.11SSU Helix 21 (h21) IL2 E.coli
168IL_11778.11
169IL_91078.11
170IL_71685.11Sarcin-like with an intercalated basepair
171IL_25181.11
172IL_09491.11
173IL_58454.11
174IL_88367.11
175IL_49976.11
176IL_52610.11
177IL_63952.11
178IL_57977.11
179IL_39324.11
180IL_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.
181IL_68827.11Reverse Kink-Turn
182IL_83920.11
183IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
184IL_06421.11Single sheared with bulged bases
185IL_20775.11tSH-inserted
186IL_71942.11
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_91044.11
194IL_87394.11
195IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
196IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
197IL_52958.11
198IL_06808.11Double sheared (tSH-tSH) one bulged base.
199IL_25314.11
200IL_20530.11
201IL_83856.11
202IL_76486.11Sarcin-ricin motif with syn G
203IL_57364.11LSU Helix 89 (H89) IL2
204IL_41139.11
205IL_06847.11Group II Intron IL
206IL_42891.11
207IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
208IL_86059.11
209IL_10365.11
210IL_06468.1116S h40 3WJ E.c.
211IL_80652.11
212IL_54450.11
213IL_13682.11
214IL_81398.11
215IL_97842.11
216IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
217IL_64589.11
218IL_54470.11tHS tHH bulge with S-turn
219IL_60649.11Kink-turn
220IL_47732.11
221IL_40845.11
222IL_43316.11
223IL_12507.11
224IL_69799.11
225IL_47687.11
226IL_55649.11
227IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
228IL_37347.11
229IL_46306.11
230IL_82601.11Tandem cWW water-inserted CU pairs
231IL_91089.11
232IL_77296.11
233IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
234IL_80505.11
235IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
236IL_75415.11Pseudo-knot forming internal loop
237IL_31224.1123S H91 IL
238IL_05221.11
239IL_06471.11
240IL_68767.11
241IL_17603.11
242IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
243IL_87523.11
244IL_03282.11
245IL_30354.11
246IL_50911.1116S h34 ILa : Part of larger motif
247IL_92280.11
248IL_06177.11cWW AG or UU
249IL_82650.11
250IL_26868.11
251IL_89794.11
252IL_28644.11
253IL_52509.11
254IL_61730.11
255IL_25082.11
256IL_53323.11
257IL_26971.11
258IL_56513.11
259IL_15205.11
260IL_21077.11
261IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
262IL_46721.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription