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_73276.522C-loop
7IL_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
8IL_65553.722Kink-turn
9IL_93424.421tSH-inserted-tHW
10IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
11IL_92027.31716S h21 S8 binding site
12IL_94430.51616S h32-h33-h34 3WJ
13IL_85647.316Sarcin-ricin parent motif with 15 Nts
14IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
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_90459.39cWW AG or UU
23IL_92114.39GAAA loop receptor "platform" motif
24IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
25IL_47444.39SRP Loop E-like motif
26IL_73000.27cHS-cWS
27IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28IL_53635.36LSU Helix 32 (H32) IL
29IL_77263.26Kink-turn from U4
30IL_97057.36
31IL_25230.36Bacterial 5S rRNA Loop E
32IL_08926.3623S H91 IL
33IL_25300.2616S h19 IL and 23S H41 IL
34IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35IL_70237.36
36IL_90133.36
37IL_13069.36LSU 3WJ H32-H33-H35A
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_72158.36LSU Helix 62 (H62) IL
40IL_86357.35LSU Helix 61 IL2
41IL_79083.35
42IL_02359.35
43IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
44IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
46IL_98591.34
47IL_22732.14tSH-inserted-tHS
48IL_31066.34SSU Helix 44 (h44) extension
49IL_94403.54LSU H77
50IL_28572.2416S h18 kink-turn like motif
51IL_45262.44
52IL_31663.1423S H73 ILa : Part of larger Motif
53IL_39526.44
54IL_82188.24LSU H68 IL from H.m.
55IL_01080.14
56IL_21333.24tSH-tHW-bulge
57IL_42251.14
58IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
59IL_39980.14
60IL_48918.34Kink-turn variant
61IL_09530.14Double S-turn motif
62IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
63IL_34363.24Kink-turn from 23S H42
64IL_38807.34
65IL_96206.23
66IL_28003.13
67IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
68IL_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.
69IL_06180.13tHS tHH bulge with S-turn
70IL_07300.23
71IL_16166.4323S H91 IL
72IL_37053.13Kink-turn from 23S H58
73IL_52173.13
74IL_62499.73
75IL_87065.1323S H91 IL | Single-Base Intercalation Site
76IL_06211.23
77IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
78IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
79IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
80IL_46034.23
81IL_79955.23SSU Helix (23) h23 IL1
82IL_58586.23
83IL_82563.13Thi-box riboswitch T-loop
84IL_98421.43SSU Helix 12 (h12) IL
85IL_43946.13
86IL_80494.23LSU H58 IL2 H.m.
87IL_05723.13
88IL_30840.23
89IL_34628.23Kink-turn
90IL_50521.12
91IL_67887.12
92IL_15840.22Triple Sheared with unpaired, inserted A
93IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
94IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
95IL_11751.12
96IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
97IL_69536.12LSU Helix 96 (H96) IL2
98IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
99IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
100IL_00998.12
101IL_16330.12
102IL_23262.42
103IL_45794.12
104IL_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)
105IL_87507.12tHS tHH bulge with S-turn
106IL_90057.12
107IL_94744.12Sarcin-ricin motif with extra cWW GA pair
108IL_97509.12Double sheared with wobble cWW.
109IL_12211.12
110IL_23414.12
111IL_31707.12Vitamin B12 aptamer
112IL_37197.12
113IL_97833.12
114IL_52940.12
115IL_65137.12Kink-turn like motif in Group I Intron
116IL_76095.32Motif from Hairpin Ribozyme
117IL_80093.12
118IL_87548.12
119IL_95150.52
120IL_21495.12
121IL_33964.12
122IL_37406.12
123IL_46435.12
124IL_80348.2223S H91 IL
125IL_90735.12
126IL_09587.12
127IL_21639.12
128IL_30381.12tHS tHH bulge with S-turn
129IL_77076.12
130IL_98566.12
131IL_09882.12
132IL_22358.12
133IL_40892.12
134IL_57364.11LSU Helix 89 (H89) IL2
135IL_60649.11Kink-turn
136IL_80505.11
137IL_83250.1116S h40 3WJ T.th.
138IL_88367.11
139IL_91078.11
140IL_02957.11
141IL_06177.11cWW AG or UU
142IL_06847.11Group II Intron IL
143IL_11302.11
144IL_20775.11tSH-inserted
145IL_25181.11
146IL_39324.11
147IL_41139.11
148IL_50911.1116S h34 ILa : Part of larger motif
149IL_53988.11
150IL_61730.11
151IL_68767.11
152IL_77296.11
153IL_80652.11
154IL_83856.11
155IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
156IL_91089.11
157IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
158IL_03110.11
159IL_21077.11
160IL_22909.11
161IL_31224.1123S H91 IL
162IL_41153.11
163IL_47687.11
164IL_54450.11
165IL_57977.11
166IL_81398.11
167IL_83920.11
168IL_89794.11
169IL_91904.11
170IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
171IL_98924.11
172IL_03282.11
173IL_11778.11
174IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
175IL_28644.11
176IL_41791.11
177IL_47732.11
178IL_52509.11
179IL_54470.11tHS tHH bulge with S-turn
180IL_63952.11
181IL_69799.11
182IL_03741.11
183IL_06306.11
184IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
185IL_52610.11
186IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
187IL_58454.11
188IL_64589.11
189IL_75415.11Pseudo-knot forming internal loop
190IL_85510.11
191IL_87523.11
192IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
193IL_05221.11
194IL_06421.11Single sheared with bulged bases
195IL_09491.11
196IL_12507.11
197IL_21421.11
198IL_23639.11tWH-tHS-L-cWW
199IL_25307.11
200IL_30067.11
201IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
202IL_37347.11
203IL_46306.11
204IL_55649.11
205IL_71685.11Sarcin-like with an intercalated basepair
206IL_97842.11
207IL_05513.11
208IL_06468.1116S h40 3WJ E.c.
209IL_17603.11
210IL_30354.11
211IL_40527.11Kink-turn
212IL_43316.11
213IL_52958.11
214IL_59529.11
215IL_71942.11
216IL_76486.11Sarcin-ricin motif with syn G
217IL_82601.11Tandem cWW water-inserted CU pairs
218IL_85805.11
219IL_02835.11
220IL_06471.11
221IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
222IL_26868.11
223IL_40845.11
224IL_46721.11
225IL_49527.11
226IL_53323.11
227IL_56513.11
228IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
229IL_66744.11SSU Helix 21 (h21) IL2 E.coli
230IL_82650.11
231IL_86059.11
232IL_88119.11
233IL_91044.11
234IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
235IL_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.
236IL_06808.11Double sheared (tSH-tSH) one bulged base.
237IL_15205.11
238IL_18675.11cWW-bulge-cWW
239IL_25082.11
240IL_26971.11
241IL_49976.11

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_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
5IL_75447.13
6IL_09520.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
7IL_19898.12
8IL_51403.12
9IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_31473.12
6IL_70401.12
7IL_33842.12
8IL_95884.12
9IL_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)
10IL_69106.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
11IL_27503.11
12IL_91956.11
13IL_34076.11
14IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)