Changes in PDB files used for clustering

Release 1.9 has 209 PDB files, release 1.10 has 213 PDB files, 209 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.10: 3WBM, 4M30, 4M4O, 4M6D.

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 1.9 has 271 motif groups, release 1.10 has 275 motif groups, 255 of them are identical.

6 motif groups were updated, 10 groups are present only in release 1.9, 14 groups are only in release 1.10.

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_39199.453Hoogsteen-edge Platform, Single bulged base
2IL_44540.443Sugar-edge, 1-base platform, consensus tHS
3IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
4IL_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
5IL_13959.426Double Sheared (tSH-tHS)
6IL_65553.722Kink-turn
7IL_73276.522C-loop
8IL_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
9IL_93424.421tSH-inserted-tHW
10IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
11IL_92027.31716S h21 S8 binding site
12IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
13IL_94430.51616S h32-h33-h34 3WJ
14IL_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
16IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
17IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
18IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
19IL_58291.410Recurrent Sub-motif found in junctions
20IL_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
21IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_47444.39SRP Loop E-like motif
23IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
24IL_90459.39cWW AG or UU
25IL_92114.39GAAA loop receptor "platform" motif
26IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
27IL_73000.27cHS-cWS
28IL_72158.36LSU Helix 62 (H62) IL
29IL_53635.36LSU Helix 32 (H32) IL
30IL_77263.26Kink-turn from U4
31IL_25230.36Bacterial 5S rRNA Loop E
32IL_97057.36
33IL_08926.3623S H91 IL
34IL_25300.2616S h19 IL and 23S H41 IL
35IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36IL_70237.36
37IL_90133.36
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_25380.16LSU Helix 89 (H89) IL2
40IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
41IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
42IL_86357.35LSU Helix 61 IL2
43IL_79083.35
44IL_02359.35
45IL_34363.24Kink-turn from 23S H42
46IL_38807.34
47IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
48IL_22732.14tSH-inserted-tHS
49IL_31066.34SSU Helix 44 (h44) extension
50IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
51IL_98591.34
52IL_28572.2416S h18 kink-turn like motif
53IL_45262.44
54IL_94403.54LSU H77
55IL_31663.1423S H73 ILa : Part of larger Motif
56IL_39526.44
57IL_01080.14
58IL_21333.24tSH-tHW-bulge
59IL_42251.14
60IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_82188.24LSU H68 IL from H.m.
62IL_39980.14
63IL_48918.34Kink-turn variant
64IL_09530.14Double S-turn motif
65IL_43946.13
66IL_98421.43SSU Helix 12 (h12) IL
67IL_05723.13
68IL_30840.23
69IL_34628.23Kink-turn
70IL_80494.23LSU H58 IL2 H.m.
71IL_28003.13
72IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
73IL_96206.23
74IL_06180.13tHS tHH bulge with S-turn
75IL_07300.23
76IL_16166.4323S H91 IL
77IL_37053.13Kink-turn from 23S H58
78IL_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.
79IL_06211.23
80IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
81IL_52173.13
82IL_62499.73
83IL_87065.1323S H91 IL | Single-Base Intercalation Site
84IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
85IL_46034.23
86IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
87IL_79955.23SSU Helix (23) h23 IL1
88IL_58586.23
89IL_82563.13Thi-box riboswitch T-loop
90IL_09587.12
91IL_21639.12
92IL_30381.12tHS tHH bulge with S-turn
93IL_80348.2223S H91 IL
94IL_90735.12
95IL_09882.12
96IL_22358.12
97IL_40892.12
98IL_77076.12
99IL_98566.12
100IL_15840.22Triple Sheared with unpaired, inserted A
101IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
102IL_50521.12
103IL_67887.12
104IL_11751.12
105IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
106IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
107IL_00998.12
108IL_16330.12
109IL_23262.42
110IL_45794.12
111IL_69536.12LSU Helix 96 (H96) IL2
112IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
113IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
114IL_12211.12
115IL_23414.12
116IL_31707.12Vitamin B12 aptamer
117IL_37197.12
118IL_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)
119IL_87507.12tHS tHH bulge with S-turn
120IL_90057.12
121IL_94744.12Sarcin-ricin motif with extra cWW GA pair
122IL_97509.12Double sheared with wobble cWW.
123IL_97833.12
124IL_21495.12
125IL_33964.12
126IL_37406.12
127IL_46435.12
128IL_52940.12
129IL_65137.12Kink-turn like motif in Group I Intron
130IL_76095.32Motif from Hairpin Ribozyme
131IL_80093.12
132IL_87548.12
133IL_95150.52
134IL_02835.11
135IL_06471.11
136IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
137IL_26868.11
138IL_40845.11
139IL_46721.11
140IL_49527.11
141IL_52958.11
142IL_59529.11
143IL_71942.11
144IL_76486.11Sarcin-ricin motif with syn G
145IL_82601.11Tandem cWW water-inserted CU pairs
146IL_85805.11
147IL_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.
148IL_06808.11Double sheared (tSH-tSH) one bulged base.
149IL_15205.11
150IL_18675.11cWW-bulge-cWW
151IL_25082.11
152IL_26971.11
153IL_49976.11
154IL_53323.11
155IL_56513.11
156IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
157IL_66744.11SSU Helix 21 (h21) IL2 E.coli
158IL_82650.11
159IL_86059.11
160IL_88119.11
161IL_91044.11
162IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
163IL_02957.11
164IL_06177.11cWW AG or UU
165IL_06847.11Group II Intron IL
166IL_11302.11
167IL_20775.11tSH-inserted
168IL_25181.11
169IL_39324.11
170IL_41139.11
171IL_57364.11LSU Helix 89 (H89) IL2
172IL_60649.11Kink-turn
173IL_80505.11
174IL_83250.1116S h40 3WJ T.th.
175IL_88367.11
176IL_91078.11
177IL_03110.11
178IL_21077.11
179IL_22909.11
180IL_31224.1123S H91 IL
181IL_41153.11
182IL_47687.11
183IL_50911.1116S h34 ILa : Part of larger motif
184IL_53988.11
185IL_61730.11
186IL_68767.11
187IL_77296.11
188IL_80652.11
189IL_83856.11
190IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
191IL_91089.11
192IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
193IL_03282.11
194IL_11778.11
195IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
196IL_28644.11
197IL_41791.11
198IL_47732.11
199IL_54450.11
200IL_57977.11
201IL_81398.11
202IL_83920.11
203IL_89794.11
204IL_91904.11
205IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
206IL_98924.11
207IL_03741.11
208IL_06306.11
209IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
210IL_52509.11
211IL_54470.11tHS tHH bulge with S-turn
212IL_63952.11
213IL_69799.11
214IL_05221.11
215IL_06421.11Single sheared with bulged bases
216IL_09491.11
217IL_12507.11
218IL_21421.11
219IL_23639.11tWH-tHS-L-cWW
220IL_25307.11
221IL_30067.11
222IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
223IL_37347.11
224IL_46306.11
225IL_52610.11
226IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
227IL_58454.11
228IL_64589.11
229IL_75415.11Pseudo-knot forming internal loop
230IL_85510.11
231IL_87523.11
232IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
233IL_05513.11
234IL_06468.1116S h40 3WJ E.c.
235IL_17603.11
236IL_30354.11
237IL_40527.11Kink-turn
238IL_43316.11
239IL_55649.11
240IL_71685.11Sarcin-like with an intercalated basepair
241IL_97842.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.102481-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.9208cWW AG or water inserted cWW Y-Y.
3IL_41766.654Tandem cWW pairs (Not AU or GC)
4IL_56465.447Single, unpaired intercalated base, consensus A
5IL_31555.513Tandem sheared with inserted, unpaired purine.
6IL_46648.61323S H91 IL | Single-Base Intercalation Site

Removed motif groups

#Motif idInstancesDescription
1IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
2IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
3IL_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)
4IL_75447.13
5IL_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
6IL_51403.12
7IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
8IL_09520.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
9IL_19898.12
10IL_90086.11

Added motif groups

#Motif idInstancesDescription
1IL_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.
2IL_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)
3IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
4IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
5IL_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)
6IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
7IL_31473.12
8IL_70401.12
9IL_33842.12
10IL_95884.12
11IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
12IL_27503.11
13IL_91956.11
14IL_34076.11