Changes in PDB files used for clustering

Release 1.6 has 204 PDB files, release 1.7 has 204 PDB files, 204 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_31555.413Tandem sheared with inserted, unpaired purine.
21IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
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_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_73000.27cHS-cWS
33IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
35IL_25380.16LSU Helix 89 (H89) IL2
36IL_53635.36LSU Helix 32 (H32) IL
37IL_70237.36
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_90133.36
40IL_72158.36LSU Helix 62 (H62) IL
41IL_08926.3623S H91 IL
42IL_25230.36Bacterial 5S rRNA Loop E
43IL_77263.26Kink-turn from U4
44IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45IL_97057.36
46IL_86357.35LSU Helix 61 IL2
47IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
48IL_25300.1516S h19 IL and 23S H41 IL
49IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
50IL_79083.35
51IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
52IL_02359.35
53IL_01080.14
54IL_39526.44
55IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
56IL_22732.14tSH-inserted-tHS
57IL_39980.14
58IL_94403.34LSU H77
59IL_98591.34
60IL_82188.24LSU H68 IL from H.m.
61IL_28572.2416S h18 kink-turn like motif
62IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
63IL_21333.24tSH-tHW-bulge
64IL_42251.14
65IL_38807.34
66IL_31663.1423S H73 ILa : Part of larger Motif
67IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
68IL_31066.34SSU Helix 44 (h44) extension
69IL_34363.24Kink-turn from 23S H42
70IL_45262.44
71IL_09530.14Double S-turn motif
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_98421.43SSU Helix 12 (h12) IL
74IL_52173.13
75IL_06211.13
76IL_07300.23
77IL_58586.23
78IL_79955.23SSU Helix (23) h23 IL1
79IL_95150.43
80IL_05723.13
81IL_43946.13
82IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
83IL_48918.23Kink-turn variant
84IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
85IL_62499.73
86IL_80494.23LSU H58 IL2 H.m.
87IL_75447.13
88IL_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.
89IL_06180.13tHS tHH bulge with S-turn
90IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
91IL_37053.13Kink-turn from 23S H58
92IL_82563.13Thi-box riboswitch T-loop
93IL_87065.1323S H91 IL | Single-Base Intercalation Site
94IL_34628.23Kink-turn
95IL_30840.23
96IL_80348.1323S H91 IL
97IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
98IL_16166.4323S H91 IL
99IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
100IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
101IL_76095.32Motif from Hairpin Ribozyme
102IL_98566.12
103IL_46034.12
104IL_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)
105IL_12211.12
106IL_21495.12
107IL_37406.12
108IL_21639.12
109IL_50521.12
110IL_01054.12
111IL_15840.22Triple Sheared with unpaired, inserted A
112IL_94744.12Sarcin-ricin motif with extra cWW GA pair
113IL_97509.12Double sheared with wobble cWW.
114IL_37197.12
115IL_96446.12
116IL_87548.12
117IL_09882.12
118IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
119IL_23262.42
120IL_69536.12LSU Helix 96 (H96) IL2
121IL_80433.12
122IL_45794.12
123IL_52940.12
124IL_77076.12
125IL_80093.12
126IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
127IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
128IL_16330.12
129IL_87507.12tHS tHH bulge with S-turn
130IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
131IL_11751.12
132IL_65137.12Kink-turn like motif in Group I Intron
133IL_19898.12
134IL_90057.12
135IL_30381.12tHS tHH bulge with S-turn
136IL_23414.12
137IL_90735.12
138IL_40892.12
139IL_33964.12
140IL_96206.12
141IL_00998.12
142IL_31707.12Vitamin B12 aptamer
143IL_97833.12
144IL_46435.12
145IL_09587.12
146IL_67887.12
147IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
148IL_88865.11
149IL_43316.11
150IL_12507.11
151IL_06468.1116S h40 3WJ E.c.
152IL_52958.11
153IL_06808.11Double sheared (tSH-tSH) one bulged base.
154IL_77014.11
155IL_03741.11
156IL_88119.11
157IL_98924.11
158IL_59529.11
159IL_91904.11
160IL_21421.11
161IL_85510.11
162IL_49527.11
163IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
164IL_47732.11
165IL_50911.1116S h34 ILa : Part of larger motif
166IL_92280.11
167IL_80505.11
168IL_69799.11
169IL_47687.11
170IL_80652.11
171IL_54450.11
172IL_71942.11
173IL_91078.11
174IL_71685.11Sarcin-like with an intercalated basepair
175IL_25181.11
176IL_09491.11
177IL_58454.11
178IL_88367.11
179IL_49976.11
180IL_57285.11
181IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
182IL_85805.11
183IL_06177.11cWW AG or UU
184IL_82650.11
185IL_31006.11tSH-tHW-L-bif-cWW
186IL_55649.11
187IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
188IL_75328.11
189IL_06306.11
190IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
191IL_23639.11tWH-tHS-L-cWW
192IL_02957.11
193IL_18675.11cWW-bulge-cWW
194IL_40527.11Kink-turn
195IL_23448.11
196IL_30354.11
197IL_83250.1116S h40 3WJ T.th.
198IL_03110.11
199IL_02835.11
200IL_25307.11
201IL_26868.11
202IL_27243.11
203IL_25314.11
204IL_20530.11
205IL_83856.11
206IL_76486.11Sarcin-ricin motif with syn G
207IL_57364.11LSU Helix 89 (H89) IL2
208IL_41139.11
209IL_91044.11
210IL_27668.11
211IL_46721.11
212IL_63952.11
213IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
214IL_41791.11
215IL_76263.11
216IL_91379.11
217IL_11302.11
218IL_89794.11
219IL_28644.11
220IL_52509.11
221IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
222IL_13682.11
223IL_81398.11
224IL_97842.11
225IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
226IL_64589.11
227IL_54470.11tHS tHH bulge with S-turn
228IL_06847.11Group II Intron IL
229IL_30067.11
230IL_41153.11
231IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
232IL_57977.11
233IL_39324.11
234IL_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.
235IL_68827.11Reverse Kink-Turn
236IL_66744.11SSU Helix 21 (h21) IL2 E.coli
237IL_53988.11
238IL_61730.11
239IL_37347.11
240IL_46306.11
241IL_82601.11Tandem cWW water-inserted CU pairs
242IL_91089.11
243IL_60649.11Kink-turn
244IL_52610.11
245IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
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_11778.11
250IL_75415.11Pseudo-knot forming internal loop
251IL_31224.1123S H91 IL
252IL_05221.11
253IL_06471.11
254IL_68767.11
255IL_17603.11
256IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
257IL_87523.11
258IL_77296.11
259IL_87394.11
260IL_40845.11
261IL_86059.11
262IL_10365.11
263IL_06421.11Single sheared with bulged bases
264IL_20775.11tSH-inserted
265IL_25082.11
266IL_53323.11
267IL_26971.11
268IL_56513.11
269IL_15205.11
270IL_21077.11
271IL_03282.11
272IL_42891.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription