Changes in PDB files used for clustering

Release 1.12 has 217 PDB files, release 1.13 has 219 PDB files, 216 of them are identical.

1 equivalence classes changed representatives: 3SD34LVZ.

2 new structures in release 1.13: 4JK0, 4NGF.

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 1.12 has 276 motif groups, release 1.13 has 278 motif groups, 271 of them are identical.

2 motif groups were updated, 3 groups are present only in release 1.12, 5 groups are only in release 1.13.

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_41766.654Tandem cWW pairs (Not AU or GC)
2IL_39199.453Hoogsteen-edge Platform, Single bulged base
3IL_56465.447Single, 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_65553.823Kink-turn
9IL_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
10IL_73276.522C-loop
11IL_93424.421tSH-inserted-tHW
12IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.31716S h21 S8 binding site
14IL_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_94430.51616S h32-h33-h34 3WJ
17IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_31555.513Tandem sheared with inserted, unpaired purine.
19IL_46648.61323S H91 IL | Single-Base Intercalation Site
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_17212.211cWW 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_37104.311Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 23S 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)
23IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_58291.410Recurrent Sub-motif found in junctions
25IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_90459.39cWW AG or UU
27IL_92114.39GAAA loop receptor "platform" motif
28IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_47444.39SRP Loop E-like motif
30IL_25300.3716S h19 IL and 23S H41 IL
31IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_73000.27cHS-cWS
33IL_46301.17Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | Tandem sheared with inserted, unpaired purine. | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_90133.36
35IL_13069.36LSU 3WJ H32-H33-H35A
36IL_25380.16LSU Helix 89 (H89) IL2
37IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
38IL_72158.36LSU Helix 62 (H62) IL
39IL_77263.26Kink-turn from U4
40IL_53635.36LSU Helix 32 (H32) IL
41IL_70173.16Single 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)
42IL_97057.36
43IL_70237.36
44IL_08926.3623S H91 IL
45IL_25230.36Bacterial 5S rRNA Loop E
46IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_02359.35
48IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
49IL_86357.35LSU Helix 61 IL2
50IL_79083.35
51IL_82188.24LSU H68 IL from H.m.
52IL_01080.14
53IL_21333.24tSH-tHW-bulge
54IL_31663.1423S H73 ILa : Part of larger Motif
55IL_48918.34Kink-turn variant
56IL_09530.14Double S-turn motif
57IL_39526.44
58IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
59IL_45262.44
60IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
61IL_39980.14
62IL_42251.14
63IL_22732.14tSH-inserted-tHS
64IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
65IL_98591.34
66IL_31066.34SSU Helix 44 (h44) extension
67IL_34363.24Kink-turn from 23S H42
68IL_38807.34
69IL_94403.54LSU H77
70IL_28572.2416S h18 kink-turn like motif
71IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
72IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
73IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
74IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
75IL_43946.13
76IL_47875.13LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
77IL_79955.23SSU Helix (23) h23 IL1
78IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
79IL_37053.13Kink-turn from 23S H58
80IL_62499.73
81IL_80348.3323S H91 IL
82IL_82563.13Thi-box riboswitch T-loop
83IL_95150.63
84IL_80494.23LSU H58 IL2 H.m.
85IL_98421.43SSU Helix 12 (h12) IL
86IL_05723.13
87IL_30840.23
88IL_58586.23
89IL_06180.13tHS tHH bulge with S-turn
90IL_07300.23
91IL_28003.13
92IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
93IL_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.
94IL_06211.33
95IL_16166.4323S H91 IL
96IL_34628.23Kink-turn
97IL_52173.13
98IL_87065.1323S H91 IL | Single-Base Intercalation Site
99IL_00998.12
100IL_12211.12
101IL_16330.12
102IL_23414.12
103IL_46435.12
104IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
105IL_67887.12
106IL_70401.12
107IL_76095.32Motif from Hairpin Ribozyme
108IL_87507.12tHS tHH bulge with S-turn
109IL_90057.12
110IL_94744.12Sarcin-ricin motif with extra cWW GA pair
111IL_97509.12Double sheared with wobble cWW.
112IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
113IL_80093.12
114IL_97833.12
115IL_24293.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 23S 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)
116IL_31707.12Vitamin B12 aptamer
117IL_52940.12
118IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
119IL_77076.12
120IL_87548.12
121IL_09587.12
122IL_21495.12
123IL_30381.12tHS tHH bulge with S-turn
124IL_37197.12
125IL_46990.12
126IL_69536.12LSU Helix 96 (H96) IL2
127IL_90735.12
128IL_09882.12
129IL_21639.12
130IL_33842.12
131IL_45794.12
132IL_96206.32
133IL_98566.12
134IL_31039.12
135IL_33964.12
136IL_37406.12
137IL_46034.32
138IL_50521.12
139IL_65137.12Kink-turn like motif in Group I Intron
140IL_11751.12
141IL_15840.22Triple Sheared with unpaired, inserted A
142IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
143IL_23262.42
144IL_40892.12
145IL_43877.12Single 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) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
146IL_03282.11
147IL_06306.11
148IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
149IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
150IL_28644.11
151IL_39324.11
152IL_41139.11
153IL_52509.11
154IL_54470.11tHS tHH bulge with S-turn
155IL_61730.11
156IL_85510.11
157IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
158IL_05221.11
159IL_06421.11Single sheared with bulged bases
160IL_09491.11
161IL_12507.11
162IL_23639.11tWH-tHS-L-cWW
163IL_41153.11
164IL_52610.11
165IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
166IL_57977.11
167IL_68767.11
168IL_71685.11Sarcin-like with an intercalated basepair
169IL_76486.11Sarcin-ricin motif with syn G
170IL_87523.11
171IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
172IL_05513.11
173IL_06468.1116S h40 3WJ E.c.
174IL_21421.11
175IL_25307.11
176IL_30067.11
177IL_46721.11
178IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
179IL_71942.11
180IL_85805.11
181IL_97842.11
182IL_06471.11
183IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
184IL_17603.11
185IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
186IL_41791.11
187IL_49527.11
188IL_52958.11
189IL_55649.11
190IL_58454.11
191IL_63952.11
192IL_82601.11Tandem cWW water-inserted CU pairs
193IL_86059.11
194IL_02835.11
195IL_06808.11Double sheared (tSH-tSH) one bulged base.
196IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
197IL_26868.11
198IL_37347.11
199IL_49976.11
200IL_53323.11
201IL_64589.11
202IL_69799.11
203IL_77296.11
204IL_80505.11
205IL_82650.11
206IL_86336.11
207IL_88119.11
208IL_91044.11
209IL_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.
210IL_06177.11cWW AG or UU
211IL_06847.11Group II Intron IL
212IL_11302.11
213IL_15205.11
214IL_18675.11cWW-bulge-cWW
215IL_25082.11
216IL_26971.11
217IL_40527.11Kink-turn
218IL_47687.11
219IL_59529.11
220IL_78513.11
221IL_80652.11
222IL_83250.1116S h40 3WJ T.th.
223IL_88367.11
224IL_91078.11
225IL_02957.11
226IL_20775.11tSH-inserted
227IL_22909.11
228IL_25181.11
229IL_40845.11
230IL_43316.11
231IL_47732.11
232IL_50911.1116S h34 ILa : Part of larger motif
233IL_53988.11
234IL_56513.11
235IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
236IL_80714.11
237IL_83856.11
238IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
239IL_91089.11
240IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
241IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
242IL_03110.11
243IL_11778.11
244IL_21077.11
245IL_31224.1123S H91 IL
246IL_46306.11
247IL_54450.11
248IL_57364.11LSU Helix 89 (H89) IL2
249IL_60649.11Kink-turn
250IL_66744.11SSU Helix 21 (h21) IL2 E.coli
251IL_70299.11
252IL_75415.11Pseudo-knot forming internal loop
253IL_81398.11
254IL_83920.11
255IL_89794.11
256IL_91904.11
257IL_98924.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.112481-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.11219cWW AG or water inserted cWW Y-Y.

Removed motif groups

#Motif idInstancesDescription
1IL_12024.12
2IL_21644.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_03741.11

Added motif groups

#Motif idInstancesDescription
1IL_12147.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
2IL_37325.11
3IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
4IL_17066.11
5IL_27640.11