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_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
7IL_65553.722Kink-turn
8IL_73276.522C-loop
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_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
18IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
19IL_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
20IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
21IL_58291.410Recurrent Sub-motif found in junctions
22IL_47444.39SRP Loop E-like motif
23IL_90459.39cWW AG or UU
24IL_92114.39GAAA loop receptor "platform" motif
25IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
26IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
27IL_73000.27cHS-cWS
28IL_25300.2616S h19 IL and 23S H41 IL
29IL_53635.36LSU Helix 32 (H32) IL
30IL_25380.16LSU Helix 89 (H89) IL2
31IL_13069.36LSU 3WJ H32-H33-H35A
32IL_90133.36
33IL_72158.36LSU Helix 62 (H62) IL
34IL_08926.3623S H91 IL
35IL_25230.36Bacterial 5S rRNA Loop E
36IL_77263.26Kink-turn from U4
37IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
38IL_70237.36
39IL_97057.36
40IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
41IL_79083.35
42IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43IL_86357.35LSU Helix 61 IL2
44IL_02359.35
45IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
46IL_09530.14Double S-turn motif
47IL_21333.24tSH-tHW-bulge
48IL_39526.44
49IL_39980.14
50IL_98591.34
51IL_28572.2416S h18 kink-turn like motif
52IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
53IL_82188.24LSU H68 IL from H.m.
54IL_31066.34SSU Helix 44 (h44) extension
55IL_48918.34Kink-turn variant
56IL_01080.14
57IL_38807.34
58IL_31663.1423S H73 ILa : Part of larger Motif
59IL_94403.54LSU H77
60IL_42251.14
61IL_34363.24Kink-turn from 23S H42
62IL_45262.44
63IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
64IL_22732.14tSH-inserted-tHS
65IL_79955.23SSU Helix (23) h23 IL1
66IL_46034.23
67IL_06180.13tHS tHH bulge with S-turn
68IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
69IL_43946.13
70IL_28003.13
71IL_30840.23
72IL_62499.73
73IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
74IL_16166.4323S H91 IL
75IL_05723.13
76IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
77IL_07300.23
78IL_96206.23
79IL_52173.13
80IL_58586.23
81IL_80494.23LSU H58 IL2 H.m.
82IL_98421.43SSU Helix 12 (h12) IL
83IL_37053.13Kink-turn from 23S H58
84IL_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.
85IL_34628.23Kink-turn
86IL_87065.1323S H91 IL | Single-Base Intercalation Site
87IL_06211.23
88IL_82563.13Thi-box riboswitch T-loop
89IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
90IL_87548.12
91IL_90057.12
92IL_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)
93IL_30381.12tHS tHH bulge with S-turn
94IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
95IL_52940.12
96IL_65137.12Kink-turn like motif in Group I Intron
97IL_37406.12
98IL_11751.12
99IL_97833.12
100IL_09587.12
101IL_21495.12
102IL_94744.12Sarcin-ricin motif with extra cWW GA pair
103IL_23414.12
104IL_80348.2223S H91 IL
105IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
106IL_76095.32Motif from Hairpin Ribozyme
107IL_80093.12
108IL_46435.12
109IL_23262.42
110IL_69536.12LSU Helix 96 (H96) IL2
111IL_21639.12
112IL_37197.12
113IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
114IL_22358.12
115IL_67887.12
116IL_45794.12
117IL_31707.12Vitamin B12 aptamer
118IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
119IL_15840.22Triple Sheared with unpaired, inserted A
120IL_16330.12
121IL_87507.12tHS tHH bulge with S-turn
122IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
123IL_00998.12
124IL_95150.52
125IL_40892.12
126IL_33964.12
127IL_50521.12
128IL_09882.12
129IL_77076.12
130IL_98566.12
131IL_12211.12
132IL_97509.12Double sheared with wobble cWW.
133IL_90735.12
134IL_83250.1116S h40 3WJ T.th.
135IL_06177.11cWW AG or UU
136IL_66744.11SSU Helix 21 (h21) IL2 E.coli
137IL_52958.11
138IL_06808.11Double sheared (tSH-tSH) one bulged base.
139IL_71942.11
140IL_31224.1123S H91 IL
141IL_05221.11
142IL_26971.11
143IL_56513.11
144IL_15205.11
145IL_21077.11
146IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
147IL_63952.11
148IL_83920.11
149IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
150IL_80652.11
151IL_54450.11
152IL_25082.11
153IL_53323.11
154IL_59529.11
155IL_91904.11
156IL_21421.11
157IL_85510.11
158IL_49527.11
159IL_30067.11
160IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
161IL_02835.11
162IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
163IL_55649.11
164IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
165IL_88119.11
166IL_98924.11
167IL_25181.11
168IL_09491.11
169IL_58454.11
170IL_88367.11
171IL_49976.11
172IL_52610.11
173IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
174IL_03110.11
175IL_41791.11
176IL_06468.1116S h40 3WJ E.c.
177IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
178IL_75415.11Pseudo-knot forming internal loop
179IL_71685.11Sarcin-like with an intercalated basepair
180IL_02957.11
181IL_18675.11cWW-bulge-cWW
182IL_40527.11Kink-turn
183IL_91044.11
184IL_47732.11
185IL_40845.11
186IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
187IL_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.
188IL_12507.11
189IL_69799.11
190IL_47687.11
191IL_89794.11
192IL_28644.11
193IL_52509.11
194IL_61730.11
195IL_06306.11
196IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
197IL_23639.11tWH-tHS-L-cWW
198IL_57364.11LSU Helix 89 (H89) IL2
199IL_41139.11
200IL_06847.11Group II Intron IL
201IL_30354.11
202IL_57977.11
203IL_39324.11
204IL_80505.11
205IL_22909.11
206IL_53988.11
207IL_03741.11
208IL_83856.11
209IL_76486.11Sarcin-ricin motif with syn G
210IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
211IL_64589.11
212IL_54470.11tHS tHH bulge with S-turn
213IL_60649.11Kink-turn
214IL_46721.11
215IL_50911.1116S h34 ILa : Part of larger motif
216IL_86059.11
217IL_43316.11
218IL_82650.11
219IL_26868.11
220IL_11778.11
221IL_91078.11
222IL_81398.11
223IL_97842.11
224IL_46306.11
225IL_82601.11Tandem cWW water-inserted CU pairs
226IL_91089.11
227IL_77296.11
228IL_41153.11
229IL_85805.11
230IL_25307.11
231IL_11302.11
232IL_06421.11Single sheared with bulged bases
233IL_20775.11tSH-inserted
234IL_37347.11
235IL_06471.11
236IL_68767.11
237IL_17603.11
238IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
239IL_87523.11
240IL_03282.11
241IL_05513.11

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_46648.61323S H91 IL | Single-Base Intercalation Site
6IL_31555.513Tandem sheared with inserted, unpaired purine.

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_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_91956.11
12IL_34076.11
13IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
14IL_27503.11