Changes in PDB files used for clustering

Release 1.8 has 206 PDB files, release 1.9 has 210 PDB files, 206 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.9: 4BW0, 4C7O, 4K27, 4LGT.

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 1.8 has 272 motif groups, release 1.9 has 271 motif groups, 251 of them are identical.

14 motif groups were updated, 7 groups are present only in release 1.8, 6 groups are only in release 1.9.

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_47174.8205cWW AG or water inserted cWW Y-Y.
2IL_39199.453Hoogsteen-edge Platform, Single bulged base
3IL_56465.346Single, 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_65553.722Kink-turn
9IL_73276.522C-loop
10IL_93424.421tSH-inserted-tHW
11IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
12IL_92027.31716S h21 S8 binding site
13IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
14IL_94430.51616S h32-h33-h34 3WJ
15IL_85647.316Sarcin-ricin parent motif with 15 Nts
16IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
17IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_31555.413Tandem sheared with inserted, unpaired purine.
19IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
20IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_58291.410Recurrent Sub-motif found in junctions
23IL_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
24IL_47444.39SRP Loop E-like motif
25IL_90459.39cWW AG or UU
26IL_92114.39GAAA loop receptor "platform" motif
27IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
29IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
30IL_73000.27cHS-cWS
31IL_13069.36LSU 3WJ H32-H33-H35A
32IL_90133.36
33IL_72158.36LSU Helix 62 (H62) IL
34IL_08926.3623S H91 IL
35IL_25230.36Bacterial 5S rRNA Loop E
36IL_25380.16LSU Helix 89 (H89) IL2
37IL_70237.36
38IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
39IL_77263.26Kink-turn from U4
40IL_97057.36
41IL_53635.36LSU Helix 32 (H32) IL
42IL_02359.35
43IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
44IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
45IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
46IL_86357.35LSU Helix 61 IL2
47IL_79083.35
48IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
49IL_21333.24tSH-tHW-bulge
50IL_39980.14
51IL_98591.34
52IL_09530.14Double S-turn motif
53IL_28572.2416S h18 kink-turn like motif
54IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
55IL_82188.24LSU H68 IL from H.m.
56IL_39526.44
57IL_31066.34SSU Helix 44 (h44) extension
58IL_01080.14
59IL_38807.34
60IL_31663.1423S H73 ILa : Part of larger Motif
61IL_42251.14
62IL_34363.24Kink-turn from 23S H42
63IL_45262.44
64IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
65IL_22732.14tSH-inserted-tHS
66IL_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)
67IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
68IL_82563.13Thi-box riboswitch T-loop
69IL_87065.1323S H91 IL | Single-Base Intercalation Site
70IL_34628.23Kink-turn
71IL_62499.73
72IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
73IL_05723.13
74IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
75IL_58586.23
76IL_52173.13
77IL_80494.23LSU H58 IL2 H.m.
78IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
79IL_98421.43SSU Helix 12 (h12) IL
80IL_37053.13Kink-turn from 23S H58
81IL_06180.13tHS tHH bulge with S-turn
82IL_30840.23
83IL_79955.23SSU Helix (23) h23 IL1
84IL_16166.4323S H91 IL
85IL_43946.13
86IL_75447.13
87IL_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.
88IL_07300.23
89IL_52940.12
90IL_65137.12Kink-turn like motif in Group I Intron
91IL_00998.12
92IL_45794.12
93IL_87507.12tHS tHH bulge with S-turn
94IL_11751.12
95IL_97833.12
96IL_30381.12tHS tHH bulge with S-turn
97IL_16330.12
98IL_33964.12
99IL_76095.32Motif from Hairpin Ribozyme
100IL_80093.12
101IL_09587.12
102IL_97509.12Double sheared with wobble cWW.
103IL_40892.12
104IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
105IL_46435.12
106IL_21495.12
107IL_37406.12
108IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
109IL_90735.12
110IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
111IL_77076.12
112IL_94744.12Sarcin-ricin motif with extra cWW GA pair
113IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
114IL_90057.12
115IL_12211.12
116IL_15840.22Triple Sheared with unpaired, inserted A
117IL_23262.42
118IL_69536.12LSU Helix 96 (H96) IL2
119IL_23414.12
120IL_96446.12
121IL_31707.12Vitamin B12 aptamer
122IL_50521.12
123IL_09882.12
124IL_98566.12
125IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
126IL_87548.12
127IL_19898.12
128IL_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)
129IL_67887.12
130IL_21639.12
131IL_37197.12
132IL_64589.11
133IL_54470.11tHS tHH bulge with S-turn
134IL_06847.11Group II Intron IL
135IL_30067.11
136IL_05513.11
137IL_63952.11
138IL_88865.11
139IL_76263.11
140IL_91379.11
141IL_66744.11SSU Helix 21 (h21) IL2 E.coli
142IL_11778.11
143IL_03741.11
144IL_06306.11
145IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
146IL_23639.11tWH-tHS-L-cWW
147IL_82601.11Tandem cWW water-inserted CU pairs
148IL_91089.11
149IL_60649.11Kink-turn
150IL_52610.11
151IL_02835.11
152IL_68827.11Reverse Kink-Turn
153IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
154IL_06421.11Single sheared with bulged bases
155IL_20775.11tSH-inserted
156IL_91078.11
157IL_83856.11
158IL_76486.11Sarcin-ricin motif with syn G
159IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
160IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
161IL_87523.11
162IL_77296.11
163IL_87394.11
164IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
165IL_03110.11
166IL_41791.11
167IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
168IL_83920.11
169IL_52958.11
170IL_06808.11Double sheared (tSH-tSH) one bulged base.
171IL_77014.11
172IL_81398.11
173IL_97842.11
174IL_46306.11
175IL_17603.11
176IL_15205.11
177IL_21077.11
178IL_03282.11
179IL_42891.11
180IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
181IL_40845.11
182IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
183IL_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.
184IL_06468.1116S h40 3WJ E.c.
185IL_80652.11
186IL_54450.11
187IL_71942.11
188IL_37347.11
189IL_06471.11
190IL_68767.11
191IL_56513.11
192IL_85510.11
193IL_49527.11
194IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
195IL_47732.11
196IL_57977.11
197IL_39324.11
198IL_43316.11
199IL_12507.11
200IL_47687.11
201IL_31006.11tSH-tHW-L-bif-cWW
202IL_55649.11
203IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
204IL_75328.11
205IL_31224.1123S H91 IL
206IL_05221.11
207IL_26971.11
208IL_21421.11
209IL_88367.11
210IL_49976.11
211IL_57285.11
212IL_30354.11
213IL_50911.1116S h34 ILa : Part of larger motif
214IL_86059.11
215IL_80505.11
216IL_69799.11
217IL_27243.11
218IL_25082.11
219IL_53323.11
220IL_59529.11
221IL_91904.11
222IL_58454.11
223IL_40527.11Kink-turn
224IL_23448.11
225IL_46721.11
226IL_85805.11
227IL_06177.11cWW AG or UU
228IL_82650.11
229IL_26868.11
230IL_89794.11
231IL_28644.11
232IL_52509.11
233IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
234IL_75415.11Pseudo-knot forming internal loop
235IL_88119.11
236IL_98924.11
237IL_25181.11
238IL_09491.11
239IL_18675.11cWW-bulge-cWW
240IL_41139.11
241IL_91044.11
242IL_27668.11
243IL_41153.11
244IL_83250.1116S h40 3WJ T.th.
245IL_25307.11
246IL_11302.11
247IL_53988.11
248IL_61730.11
249IL_71685.11Sarcin-like with an intercalated basepair
250IL_02957.11
251IL_57364.11LSU Helix 89 (H89) IL2

Updated motif groups

#Motif idInstancesDescription
1IL_97217.92471-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_41766.552Tandem cWW pairs (Not AU or GC)
3IL_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
4IL_46648.51223S H91 IL | Single-Base Intercalation Site
5IL_25300.2616S h19 IL and 23S H41 IL
6IL_94403.54LSU H77
7IL_48918.34Kink-turn variant
8IL_96206.23
9IL_46034.23
10IL_06211.23
11IL_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
12IL_09520.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
13IL_95150.52
14IL_80348.2223S H91 IL

Removed motif groups

#Motif idInstancesDescription
1IL_39674.14LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_80433.12
3IL_01054.12
4IL_20530.11
5IL_25314.11
6IL_92280.11
7IL_13682.11

Added motif groups

#Motif idInstancesDescription
1IL_28003.13
2IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_51403.12
4IL_22358.12
5IL_90086.11
6IL_22909.11