Changes in PDB files used for clustering

Release 1.8 has 205 PDB files, release 1.9 has 209 PDB files, 205 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_73276.522C-loop
9IL_65553.722Kink-turn
10IL_93424.421tSH-inserted-tHW
11IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
12IL_92027.31716S h21 S8 binding site
13IL_85647.316Sarcin-ricin parent motif with 15 Nts
14IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
15IL_94430.51616S h32-h33-h34 3WJ
16IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
17IL_31555.413Tandem sheared with inserted, unpaired purine.
18IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
20IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
21IL_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
22IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_58291.410Recurrent Sub-motif found in junctions
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_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
29IL_73000.27cHS-cWS
30IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31IL_13069.36LSU 3WJ H32-H33-H35A
32IL_72158.36LSU Helix 62 (H62) IL
33IL_97057.36
34IL_77263.26Kink-turn from U4
35IL_25230.36Bacterial 5S rRNA Loop E
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_08926.3623S H91 IL
38IL_70237.36
39IL_25380.16LSU Helix 89 (H89) IL2
40IL_53635.36LSU Helix 32 (H32) IL
41IL_90133.36
42IL_02359.35
43IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
44IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
45IL_86357.35LSU Helix 61 IL2
46IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
47IL_79083.35
48IL_09530.14Double S-turn motif
49IL_21333.24tSH-tHW-bulge
50IL_31066.34SSU Helix 44 (h44) extension
51IL_98591.34
52IL_28572.2416S h18 kink-turn like motif
53IL_45262.44
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_31663.1423S H73 ILa : Part of larger Motif
56IL_39526.44
57IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
58IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
59IL_22732.14tSH-inserted-tHS
60IL_42251.14
61IL_39980.14
62IL_82188.24LSU H68 IL from H.m.
63IL_01080.14
64IL_34363.24Kink-turn from 23S H42
65IL_38807.34
66IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
67IL_34628.23Kink-turn
68IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
69IL_52173.13
70IL_80494.23LSU H58 IL2 H.m.
71IL_37053.13Kink-turn from 23S H58
72IL_62499.73
73IL_05723.13
74IL_07300.23
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_06180.13tHS tHH bulge with S-turn
77IL_16166.4323S H91 IL
78IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
79IL_58586.23
80IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
81IL_87065.1323S H91 IL | Single-Base Intercalation Site
82IL_98421.43SSU Helix 12 (h12) IL
83IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
84IL_30840.23
85IL_43946.13
86IL_75447.13
87IL_79955.23SSU Helix (23) h23 IL1
88IL_82563.13Thi-box riboswitch T-loop
89IL_40892.12
90IL_67887.12
91IL_76095.32Motif from Hairpin Ribozyme
92IL_80093.12
93IL_87548.12
94IL_09587.12
95IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
96IL_90735.12
97IL_09882.12
98IL_21495.12
99IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
100IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
101IL_77076.12
102IL_21639.12
103IL_45794.12
104IL_69536.12LSU Helix 96 (H96) IL2
105IL_97509.12Double sheared with wobble cWW.
106IL_11751.12
107IL_15840.22Triple Sheared with unpaired, inserted A
108IL_19898.12
109IL_31707.12Vitamin B12 aptamer
110IL_37197.12
111IL_52940.12
112IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
113IL_97833.12
114IL_23262.42
115IL_46435.12
116IL_65137.12Kink-turn like motif in Group I Intron
117IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
118IL_94744.12Sarcin-ricin motif with extra cWW GA pair
119IL_00998.12
120IL_12211.12
121IL_16330.12
122IL_23414.12
123IL_30381.12tHS tHH bulge with S-turn
124IL_33964.12
125IL_37406.12
126IL_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)
127IL_87507.12tHS tHH bulge with S-turn
128IL_90057.12
129IL_50521.12
130IL_98566.12
131IL_05221.11
132IL_06468.1116S h40 3WJ E.c.
133IL_26868.11
134IL_50911.1116S h34 ILa : Part of larger motif
135IL_53988.11
136IL_57364.11LSU Helix 89 (H89) IL2
137IL_60649.11Kink-turn
138IL_71942.11
139IL_82601.11Tandem cWW water-inserted CU pairs
140IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
141IL_05513.11
142IL_06471.11
143IL_17603.11
144IL_21421.11
145IL_26971.11
146IL_31224.1123S H91 IL
147IL_39324.11
148IL_41139.11
149IL_47687.11
150IL_54450.11
151IL_61730.11
152IL_68767.11
153IL_76486.11Sarcin-ricin motif with syn G
154IL_82650.11
155IL_85805.11
156IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
157IL_02835.11
158IL_06808.11Double sheared (tSH-tSH) one bulged base.
159IL_15205.11
160IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
161IL_25082.11
162IL_41153.11
163IL_47732.11
164IL_52509.11
165IL_54470.11tHS tHH bulge with S-turn
166IL_57977.11
167IL_80505.11
168IL_83250.1116S h40 3WJ T.th.
169IL_86059.11
170IL_88119.11
171IL_91044.11
172IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
173IL_98924.11
174IL_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.
175IL_06847.11Group II Intron IL
176IL_11302.11
177IL_18675.11cWW-bulge-cWW
178IL_25181.11
179IL_28644.11
180IL_41791.11
181IL_52610.11
182IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
183IL_63952.11
184IL_80652.11
185IL_88367.11
186IL_91078.11
187IL_02957.11
188IL_06177.11cWW AG or UU
189IL_30067.11
190IL_46306.11
191IL_55649.11
192IL_58454.11
193IL_64589.11
194IL_69799.11
195IL_77296.11
196IL_81398.11
197IL_83856.11
198IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
199IL_91089.11
200IL_03110.11
201IL_11778.11
202IL_20775.11tSH-inserted
203IL_30354.11
204IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
205IL_37347.11
206IL_49527.11
207IL_52958.11
208IL_83920.11
209IL_89794.11
210IL_91904.11
211IL_97842.11
212IL_03282.11
213IL_06306.11
214IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
215IL_21077.11
216IL_25307.11
217IL_40527.11Kink-turn
218IL_43316.11
219IL_46721.11
220IL_49976.11
221IL_53323.11
222IL_59529.11
223IL_75415.11Pseudo-knot forming internal loop
224IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
225IL_03741.11
226IL_06421.11Single sheared with bulged bases
227IL_09491.11
228IL_12507.11
229IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
230IL_23639.11tWH-tHS-L-cWW
231IL_40845.11
232IL_56513.11
233IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
234IL_66744.11SSU Helix 21 (h21) IL2 E.coli
235IL_71685.11Sarcin-like with an intercalated basepair
236IL_85510.11
237IL_87523.11

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