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_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_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
23IL_46648.41123S H91 IL | Single-Base Intercalation Site
24IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_13069.36LSU 3WJ H32-H33-H35A
36IL_90133.36
37IL_72158.36LSU Helix 62 (H62) IL
38IL_08926.3623S H91 IL
39IL_70237.36
40IL_25230.36Bacterial 5S rRNA Loop E
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_25380.16LSU Helix 89 (H89) IL2
43IL_77263.26Kink-turn from U4
44IL_97057.36
45IL_53635.36LSU Helix 32 (H32) 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_39980.14
54IL_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)
55IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
56IL_22732.14tSH-inserted-tHS
57IL_98591.34
58IL_94403.34LSU H77
59IL_82188.24LSU H68 IL from H.m.
60IL_42251.14
61IL_38807.34
62IL_31663.1423S H73 ILa : Part of larger Motif
63IL_09530.14Double S-turn motif
64IL_28572.2416S h18 kink-turn like motif
65IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
66IL_21333.24tSH-tHW-bulge
67IL_34363.24Kink-turn from 23S H42
68IL_45262.44
69IL_39526.44
70IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
71IL_31066.34SSU Helix 44 (h44) extension
72IL_01080.14
73IL_06211.13
74IL_58586.23
75IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
76IL_05723.13
77IL_43946.13
78IL_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.
79IL_34628.23Kink-turn
80IL_79955.23SSU Helix (23) h23 IL1
81IL_95150.43
82IL_75447.13
83IL_87065.1323S H91 IL | Single-Base Intercalation Site
84IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
85IL_07300.23
86IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
87IL_80494.23LSU H58 IL2 H.m.
88IL_82563.13Thi-box riboswitch T-loop
89IL_62499.73
90IL_37053.13Kink-turn from 23S H58
91IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
92IL_48918.23Kink-turn variant
93IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
94IL_80348.1323S H91 IL
95IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
96IL_16166.4323S H91 IL
97IL_06180.13tHS tHH bulge with S-turn
98IL_98421.43SSU Helix 12 (h12) IL
99IL_52173.13
100IL_30840.23
101IL_67887.12
102IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
103IL_50521.12
104IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
105IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
106IL_46034.12
107IL_87548.12
108IL_09882.12
109IL_80093.12
110IL_30381.12tHS tHH bulge with S-turn
111IL_00998.12
112IL_21639.12
113IL_52940.12
114IL_77076.12
115IL_97509.12Double sheared with wobble cWW.
116IL_37197.12
117IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
118IL_11751.12
119IL_65137.12Kink-turn like motif in Group I Intron
120IL_19898.12
121IL_90057.12
122IL_96206.12
123IL_09587.12
124IL_80433.12
125IL_45794.12
126IL_46435.12
127IL_37406.12
128IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
129IL_16330.12
130IL_87507.12tHS tHH bulge with S-turn
131IL_31707.12Vitamin B12 aptamer
132IL_97833.12
133IL_98566.12
134IL_21495.12
135IL_94744.12Sarcin-ricin motif with extra cWW GA pair
136IL_23414.12
137IL_90735.12
138IL_40892.12
139IL_33964.12
140IL_76095.32Motif from Hairpin Ribozyme
141IL_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)
142IL_12211.12
143IL_01054.12
144IL_15840.22Triple Sheared with unpaired, inserted A
145IL_23262.42
146IL_69536.12LSU Helix 96 (H96) IL2
147IL_50911.1116S h34 ILa : Part of larger motif
148IL_92280.11
149IL_06177.11cWW AG or UU
150IL_82650.11
151IL_26868.11
152IL_89794.11
153IL_28644.11
154IL_52509.11
155IL_61730.11
156IL_25082.11
157IL_53323.11
158IL_26971.11
159IL_56513.11
160IL_15205.11
161IL_21077.11
162IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
163IL_46721.11
164IL_85805.11
165IL_03110.11
166IL_02835.11
167IL_25307.11
168IL_11302.11
169IL_53988.11
170IL_03741.11
171IL_88119.11
172IL_98924.11
173IL_59529.11
174IL_91904.11
175IL_21421.11
176IL_85510.11
177IL_49527.11
178IL_30067.11
179IL_41153.11
180IL_83250.1116S h40 3WJ T.th.
181IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
182IL_41791.11
183IL_76263.11
184IL_66744.11SSU Helix 21 (h21) IL2 E.coli
185IL_11778.11
186IL_91078.11
187IL_71685.11Sarcin-like with an intercalated basepair
188IL_25181.11
189IL_09491.11
190IL_58454.11
191IL_88367.11
192IL_49976.11
193IL_52610.11
194IL_63952.11
195IL_57977.11
196IL_39324.11
197IL_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.
198IL_68827.11Reverse Kink-Turn
199IL_83920.11
200IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
201IL_06421.11Single sheared with bulged bases
202IL_20775.11tSH-inserted
203IL_71942.11
204IL_06306.11
205IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
206IL_23639.11tWH-tHS-L-cWW
207IL_02957.11
208IL_18675.11cWW-bulge-cWW
209IL_40527.11Kink-turn
210IL_91044.11
211IL_87394.11
212IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
213IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
214IL_52958.11
215IL_06808.11Double sheared (tSH-tSH) one bulged base.
216IL_25314.11
217IL_20530.11
218IL_83856.11
219IL_76486.11Sarcin-ricin motif with syn G
220IL_57364.11LSU Helix 89 (H89) IL2
221IL_41139.11
222IL_06847.11Group II Intron IL
223IL_42891.11
224IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
225IL_86059.11
226IL_10365.11
227IL_06468.1116S h40 3WJ E.c.
228IL_80652.11
229IL_54450.11
230IL_13682.11
231IL_81398.11
232IL_97842.11
233IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
234IL_64589.11
235IL_54470.11tHS tHH bulge with S-turn
236IL_60649.11Kink-turn
237IL_47732.11
238IL_40845.11
239IL_43316.11
240IL_12507.11
241IL_69799.11
242IL_47687.11
243IL_55649.11
244IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
245IL_37347.11
246IL_46306.11
247IL_82601.11Tandem cWW water-inserted CU pairs
248IL_91089.11
249IL_77296.11
250IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
251IL_80505.11
252IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
253IL_75415.11Pseudo-knot forming internal loop
254IL_31224.1123S H91 IL
255IL_05221.11
256IL_06471.11
257IL_68767.11
258IL_17603.11
259IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
260IL_87523.11
261IL_03282.11
262IL_30354.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription