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

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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_73276.421C-loop
12IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
13IL_93424.421tSH-inserted-tHW
14IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_94430.51616S h32-h33-h34 3WJ
18IL_85647.316Sarcin-ricin parent motif with 15 Nts
19IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_31555.413Tandem sheared with inserted, unpaired purine.
22IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_46648.41123S H91 IL | Single-Base Intercalation Site
25IL_58291.410Recurrent Sub-motif found in junctions
26IL_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
27IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
28IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_92114.39GAAA loop receptor "platform" motif
30IL_47444.39SRP Loop E-like motif
31IL_90459.39cWW AG or UU
32IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_73000.27cHS-cWS
35IL_77263.26Kink-turn from U4
36IL_97057.36
37IL_53635.36LSU Helix 32 (H32) IL
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_90133.36
40IL_72158.36LSU Helix 62 (H62) IL
41IL_08926.3623S H91 IL
42IL_70237.36
43IL_25230.36Bacterial 5S rRNA Loop E
44IL_25380.16LSU Helix 89 (H89) IL2
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_05684.15tHS tHH bulge with S-turn | Double S-turn motif
48IL_86357.35LSU Helix 61 IL2
49IL_79083.35
50IL_02359.35
51IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
52IL_25300.1516S h19 IL and 23S H41 IL
53IL_28572.2416S h18 kink-turn like motif
54IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
55IL_21333.24tSH-tHW-bulge
56IL_34363.24Kink-turn from 23S H42
57IL_45262.44
58IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
59IL_31066.34SSU Helix 44 (h44) extension
60IL_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)
61IL_01080.14
62IL_39980.14
63IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
64IL_22732.14tSH-inserted-tHS
65IL_98591.34
66IL_94403.34LSU H77
67IL_82188.24LSU H68 IL from H.m.
68IL_09530.14Double S-turn motif
69IL_39526.44
70IL_42251.14
71IL_38807.34
72IL_31663.1423S H73 ILa : Part of larger Motif
73IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
74IL_30840.23
75IL_80348.1323S H91 IL
76IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
77IL_16166.4323S H91 IL
78IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
79IL_98421.43SSU Helix 12 (h12) IL
80IL_52173.13
81IL_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.
82IL_34628.23Kink-turn
83IL_06211.13
84IL_58586.23
85IL_75447.13
86IL_87065.1323S H91 IL | Single-Base Intercalation Site
87IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
88IL_07300.23
89IL_05723.13
90IL_43946.13
91IL_82563.13Thi-box riboswitch T-loop
92IL_79955.23SSU Helix (23) h23 IL1
93IL_95150.43
94IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
95IL_48918.23Kink-turn variant
96IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
97IL_80494.23LSU H58 IL2 H.m.
98IL_62499.73
99IL_37053.13Kink-turn from 23S H58
100IL_06180.13tHS tHH bulge with S-turn
101IL_01054.12
102IL_15840.22Triple Sheared with unpaired, inserted A
103IL_23262.42
104IL_69536.12LSU Helix 96 (H96) IL2
105IL_31707.12Vitamin B12 aptamer
106IL_97833.12
107IL_98566.12
108IL_67887.12
109IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
110IL_76095.32Motif from Hairpin Ribozyme
111IL_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)
112IL_12211.12
113IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
114IL_46034.12
115IL_30381.12tHS tHH bulge with S-turn
116IL_00998.12
117IL_21639.12
118IL_50521.12
119IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
120IL_97509.12Double sheared with wobble cWW.
121IL_37197.12
122IL_87548.12
123IL_09882.12
124IL_80093.12
125IL_09587.12
126IL_80433.12
127IL_45794.12
128IL_52940.12
129IL_77076.12
130IL_46435.12
131IL_37406.12
132IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
133IL_16330.12
134IL_87507.12tHS tHH bulge with S-turn
135IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
136IL_11751.12
137IL_65137.12Kink-turn like motif in Group I Intron
138IL_19898.12
139IL_90057.12
140IL_96206.12
141IL_21495.12
142IL_94744.12Sarcin-ricin motif with extra cWW GA pair
143IL_23414.12
144IL_90735.12
145IL_40892.12
146IL_33964.12
147IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
148IL_86059.11
149IL_10365.11
150IL_80505.11
151IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
152IL_75415.11Pseudo-knot forming internal loop
153IL_31224.1123S H91 IL
154IL_05221.11
155IL_06471.11
156IL_68767.11
157IL_17603.11
158IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
159IL_87523.11
160IL_03282.11
161IL_41153.11
162IL_40845.11
163IL_43316.11
164IL_82650.11
165IL_26868.11
166IL_89794.11
167IL_28644.11
168IL_52509.11
169IL_61730.11
170IL_25082.11
171IL_53323.11
172IL_26971.11
173IL_56513.11
174IL_15205.11
175IL_21077.11
176IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
177IL_25307.11
178IL_11302.11
179IL_53988.11
180IL_03741.11
181IL_88119.11
182IL_98924.11
183IL_59529.11
184IL_91904.11
185IL_21421.11
186IL_85510.11
187IL_49527.11
188IL_30067.11
189IL_50911.1116S h34 ILa : Part of larger motif
190IL_92280.11
191IL_06177.11cWW AG or UU
192IL_66744.11SSU Helix 21 (h21) IL2 E.coli
193IL_11778.11
194IL_91078.11
195IL_71685.11Sarcin-like with an intercalated basepair
196IL_25181.11
197IL_09491.11
198IL_58454.11
199IL_88367.11
200IL_49976.11
201IL_52610.11
202IL_85805.11
203IL_03110.11
204IL_02835.11
205IL_83920.11
206IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
207IL_06421.11Single sheared with bulged bases
208IL_20775.11tSH-inserted
209IL_71942.11
210IL_06306.11
211IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
212IL_23639.11tWH-tHS-L-cWW
213IL_02957.11
214IL_18675.11cWW-bulge-cWW
215IL_40527.11Kink-turn
216IL_91044.11
217IL_47732.11
218IL_83250.1116S h40 3WJ T.th.
219IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
220IL_41791.11
221IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
222IL_52958.11
223IL_06808.11Double sheared (tSH-tSH) one bulged base.
224IL_25314.11
225IL_20530.11
226IL_83856.11
227IL_76486.11Sarcin-ricin motif with syn G
228IL_57364.11LSU Helix 89 (H89) IL2
229IL_41139.11
230IL_06847.11Group II Intron IL
231IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
232IL_63952.11
233IL_57977.11
234IL_39324.11
235IL_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.
236IL_06468.1116S h40 3WJ E.c.
237IL_80652.11
238IL_54450.11
239IL_13682.11
240IL_81398.11
241IL_97842.11
242IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
243IL_64589.11
244IL_54470.11tHS tHH bulge with S-turn
245IL_60649.11Kink-turn
246IL_30354.11
247IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
248IL_12507.11
249IL_69799.11
250IL_47687.11
251IL_55649.11
252IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
253IL_37347.11
254IL_46306.11
255IL_82601.11Tandem cWW water-inserted CU pairs
256IL_91089.11
257IL_77296.11
258IL_46721.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription