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_73276.522C-loop
10IL_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
11IL_93424.421tSH-inserted-tHW
12IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.31716S h21 S8 binding site
14IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
15IL_94430.51616S h32-h33-h34 3WJ
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_46648.61323S H91 IL | Single-Base Intercalation Site
19IL_31555.513Tandem sheared with inserted, unpaired purine.
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
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_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
24IL_58291.410Recurrent Sub-motif found in junctions
25IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_92114.39GAAA loop receptor "platform" motif
27IL_47444.39SRP Loop E-like motif
28IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_90459.39cWW AG or UU
30IL_73000.27cHS-cWS
31IL_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.
32IL_25300.3716S h19 IL and 23S H41 IL
33IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_25380.16LSU Helix 89 (H89) IL2
35IL_70237.36
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_25230.36Bacterial 5S rRNA Loop E
38IL_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)
39IL_97057.36
40IL_77263.26Kink-turn from U4
41IL_53635.36LSU Helix 32 (H32) IL
42IL_08926.3623S H91 IL
43IL_13069.36LSU 3WJ H32-H33-H35A
44IL_90133.36
45IL_72158.36LSU Helix 62 (H62) IL
46IL_02359.35
47IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
48IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
49IL_86357.35LSU Helix 61 IL2
50IL_79083.35
51IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
52IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
53IL_98591.34
54IL_09530.14Double S-turn motif
55IL_48918.34Kink-turn variant
56IL_01080.14
57IL_82188.24LSU H68 IL from H.m.
58IL_39526.44
59IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60IL_22732.14tSH-inserted-tHS
61IL_94403.54LSU H77
62IL_42251.14
63IL_38807.34
64IL_31663.1423S H73 ILa : Part of larger Motif
65IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
66IL_34363.24Kink-turn from 23S H42
67IL_45262.44
68IL_28572.2416S h18 kink-turn like motif
69IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
70IL_21333.24tSH-tHW-bulge
71IL_31066.34SSU Helix 44 (h44) extension
72IL_39980.14
73IL_98421.43SSU Helix 12 (h12) IL
74IL_05723.13
75IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
76IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
77IL_06211.33
78IL_52173.13
79IL_58586.23
80IL_80494.23LSU H58 IL2 H.m.
81IL_79955.23SSU Helix (23) h23 IL1
82IL_37053.13Kink-turn from 23S H58
83IL_28003.13
84IL_06180.13tHS tHH bulge with S-turn
85IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
86IL_95150.63
87IL_30840.23
88IL_62499.73
89IL_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.
90IL_07300.23
91IL_80348.3323S H91 IL
92IL_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
93IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
94IL_16166.4323S H91 IL
95IL_43946.13
96IL_82563.13Thi-box riboswitch T-loop
97IL_87065.1323S H91 IL | Single-Base Intercalation Site
98IL_34628.23Kink-turn
99IL_76095.32Motif from Hairpin Ribozyme
100IL_09587.12
101IL_97509.12Double sheared with wobble cWW.
102IL_45794.12
103IL_80093.12
104IL_46435.12
105IL_16330.12
106IL_87507.12tHS tHH bulge with S-turn
107IL_50521.12
108IL_21495.12
109IL_37406.12
110IL_46990.12
111IL_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)
112IL_90735.12
113IL_40892.12
114IL_33964.12
115IL_87548.12
116IL_96206.32
117IL_15840.22Triple Sheared with unpaired, inserted A
118IL_52940.12
119IL_09882.12
120IL_77076.12
121IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
122IL_23262.42
123IL_69536.12LSU Helix 96 (H96) IL2
124IL_94744.12Sarcin-ricin motif with extra cWW GA pair
125IL_23414.12
126IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
127IL_70401.12
128IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
129IL_11751.12
130IL_90057.12
131IL_98566.12
132IL_12211.12
133IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
134IL_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)
135IL_46034.32
136IL_33842.12
137IL_65137.12Kink-turn like motif in Group I Intron
138IL_30381.12tHS tHH bulge with S-turn
139IL_31039.12
140IL_67887.12
141IL_21639.12
142IL_31707.12Vitamin B12 aptamer
143IL_97833.12
144IL_00998.12
145IL_37197.12
146IL_03110.11
147IL_02835.11
148IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
149IL_06421.11Single sheared with bulged bases
150IL_20775.11tSH-inserted
151IL_83856.11
152IL_76486.11Sarcin-ricin motif with syn G
153IL_70299.11
154IL_57364.11LSU Helix 89 (H89) IL2
155IL_41139.11
156IL_91044.11
157IL_47732.11
158IL_50911.1116S h34 ILa : Part of larger motif
159IL_80714.11
160IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
161IL_41791.11
162IL_06468.1116S h40 3WJ E.c.
163IL_52958.11
164IL_06808.11Double sheared (tSH-tSH) one bulged base.
165IL_71942.11
166IL_86336.11
167IL_81398.11
168IL_97842.11
169IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
170IL_64589.11
171IL_54470.11tHS tHH bulge with S-turn
172IL_06847.11Group II Intron IL
173IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
174IL_85805.11
175IL_57977.11
176IL_39324.11
177IL_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.
178IL_12507.11
179IL_69799.11
180IL_47687.11
181IL_80652.11
182IL_54450.11
183IL_37347.11
184IL_46306.11
185IL_82601.11Tandem cWW water-inserted CU pairs
186IL_91089.11
187IL_60649.11Kink-turn
188IL_46721.11
189IL_83250.1116S h40 3WJ T.th.
190IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
191IL_80505.11
192IL_22909.11
193IL_55649.11
194IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
195IL_31224.1123S H91 IL
196IL_05221.11
197IL_06471.11
198IL_68767.11
199IL_17603.11
200IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
201IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
202IL_77296.11
203IL_41153.11
204IL_63952.11
205IL_86059.11
206IL_43316.11
207IL_82650.11
208IL_26868.11
209IL_25082.11
210IL_53323.11
211IL_26971.11
212IL_56513.11
213IL_15205.11
214IL_87523.11
215IL_03282.11
216IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
217IL_25307.11
218IL_11302.11
219IL_89794.11
220IL_28644.11
221IL_52509.11
222IL_75415.11Pseudo-knot forming internal loop
223IL_88119.11
224IL_98924.11
225IL_59529.11
226IL_91904.11
227IL_21421.11
228IL_85510.11
229IL_21077.11
230IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
231IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
232IL_06177.11cWW AG or UU
233IL_66744.11SSU Helix 21 (h21) IL2 E.coli
234IL_53988.11
235IL_61730.11
236IL_71685.11Sarcin-like with an intercalated basepair
237IL_25181.11
238IL_09491.11
239IL_58454.11
240IL_88367.11
241IL_49527.11
242IL_30067.11
243IL_05513.11
244IL_40845.11
245IL_83920.11
246IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
247IL_11778.11
248IL_91078.11
249IL_06306.11
250IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
251IL_23639.11tWH-tHS-L-cWW
252IL_02957.11
253IL_18675.11cWW-bulge-cWW
254IL_40527.11Kink-turn
255IL_49976.11
256IL_52610.11
257IL_78513.11

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_17066.11
3IL_27640.11
4IL_37325.11
5IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)