Changes in PDB files used for clustering

Release 1.7 has 203 PDB files, release 1.8 has 205 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 1.8: 4L8H, 4MGN.

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 1.7 has 272 motif groups, release 1.8 has 272 motif groups, 266 of them are identical.

3 motif groups were updated, 3 groups are present only in release 1.7, 3 groups are only in release 1.8.

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_47174.8205cWW AG or water inserted cWW Y-Y.
2IL_39199.453Hoogsteen-edge Platform, Single bulged base
3IL_41766.449Tandem cWW pairs (Not AU or GC)
4IL_56465.346Single, unpaired intercalated base, consensus A
5IL_44540.443Sugar-edge, 1-base platform, consensus tHS
6IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_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
8IL_13959.426Double Sheared (tSH-tHS)
9IL_65553.722Kink-turn
10IL_28947.12123S H91 IL | 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_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_31555.413Tandem sheared with inserted, unpaired purine.
19IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
20IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
22IL_46648.41123S H91 IL | Single-Base Intercalation Site
23IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
24IL_58291.410Recurrent Sub-motif found in junctions
25IL_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
26IL_47444.39SRP Loop E-like motif
27IL_92114.39GAAA loop receptor "platform" motif
28IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_90459.39cWW AG or UU
30IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_73000.27cHS-cWS
33IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
34IL_25230.36Bacterial 5S rRNA Loop E
35IL_97057.36
36IL_53635.36LSU Helix 32 (H32) IL
37IL_77263.26Kink-turn from U4
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_90133.36
40IL_72158.36LSU Helix 62 (H62) IL
41IL_08926.3623S H91 IL
42IL_25380.16LSU Helix 89 (H89) IL2
43IL_70237.36
44IL_25300.1516S h19 IL and 23S H41 IL
45IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
46IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_86357.35LSU Helix 61 IL2
48IL_79083.35
49IL_02359.35
50IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
51IL_42251.14
52IL_38807.34
53IL_31663.1423S H73 ILa : Part of larger Motif
54IL_34363.24Kink-turn from 23S H42
55IL_45262.44
56IL_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)
57IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
58IL_21333.24tSH-tHW-bulge
59IL_28572.2416S h18 kink-turn like motif
60IL_31066.34SSU Helix 44 (h44) extension
61IL_01080.14
62IL_39980.14
63IL_98591.34
64IL_09530.14Double S-turn motif
65IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
66IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67IL_22732.14tSH-inserted-tHS
68IL_82188.24LSU H68 IL from H.m.
69IL_39526.44
70IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
71IL_37053.13Kink-turn from 23S H58
72IL_30840.23
73IL_62499.73
74IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
75IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
76IL_16166.4323S H91 IL
77IL_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.
78IL_34628.23Kink-turn
79IL_75447.13
80IL_87065.1323S H91 IL | Single-Base Intercalation Site
81IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
82IL_07300.23
83IL_52173.13
84IL_58586.23
85IL_43946.13
86IL_82563.13Thi-box riboswitch T-loop
87IL_80348.1323S H91 IL
88IL_05723.13
89IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
90IL_48918.23Kink-turn variant
91IL_98421.43SSU Helix 12 (h12) IL
92IL_06211.13
93IL_79955.23SSU Helix (23) h23 IL1
94IL_95150.43
95IL_80494.23LSU H58 IL2 H.m.
96IL_06180.13tHS tHH bulge with S-turn
97IL_87548.12
98IL_52940.12
99IL_90057.12
100IL_96206.12
101IL_01054.12
102IL_15840.22Triple Sheared with unpaired, inserted A
103IL_23262.42
104IL_69536.12LSU Helix 96 (H96) IL2
105IL_11751.12
106IL_65137.12Kink-turn like motif in Group I Intron
107IL_19898.12
108IL_67887.12
109IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
110IL_98566.12
111IL_12211.12
112IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
113IL_46034.12
114IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
115IL_97833.12
116IL_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)
117IL_30381.12tHS tHH bulge with S-turn
118IL_00998.12
119IL_21639.12
120IL_76095.32Motif from Hairpin Ribozyme
121IL_97509.12Double sheared with wobble cWW.
122IL_37197.12
123IL_31707.12Vitamin B12 aptamer
124IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
125IL_09587.12
126IL_80433.12
127IL_45794.12
128IL_80093.12
129IL_46435.12
130IL_37406.12
131IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
132IL_16330.12
133IL_87507.12tHS tHH bulge with S-turn
134IL_50521.12
135IL_09882.12
136IL_77076.12
137IL_21495.12
138IL_94744.12Sarcin-ricin motif with extra cWW GA pair
139IL_23414.12
140IL_90735.12
141IL_40892.12
142IL_33964.12
143IL_80505.11
144IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
145IL_75415.11Pseudo-knot forming internal loop
146IL_31224.1123S H91 IL
147IL_05221.11
148IL_06471.11
149IL_68767.11
150IL_17603.11
151IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
152IL_87523.11
153IL_03282.11
154IL_63952.11
155IL_86059.11
156IL_43316.11
157IL_82650.11
158IL_26868.11
159IL_89794.11
160IL_28644.11
161IL_52509.11
162IL_61730.11
163IL_25082.11
164IL_53323.11
165IL_26971.11
166IL_56513.11
167IL_15205.11
168IL_21077.11
169IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
170IL_25307.11
171IL_11302.11
172IL_53988.11
173IL_03741.11
174IL_88119.11
175IL_98924.11
176IL_59529.11
177IL_91904.11
178IL_21421.11
179IL_85510.11
180IL_49527.11
181IL_30067.11
182IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
183IL_40845.11
184IL_06177.11cWW AG or UU
185IL_66744.11SSU Helix 21 (h21) IL2 E.coli
186IL_11778.11
187IL_91078.11
188IL_71685.11Sarcin-like with an intercalated basepair
189IL_25181.11
190IL_09491.11
191IL_58454.11
192IL_88367.11
193IL_49976.11
194IL_52610.11
195IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
196IL_83920.11
197IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
198IL_06421.11Single sheared with bulged bases
199IL_20775.11tSH-inserted
200IL_71942.11
201IL_06306.11
202IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
203IL_23639.11tWH-tHS-L-cWW
204IL_02957.11
205IL_18675.11cWW-bulge-cWW
206IL_40527.11Kink-turn
207IL_91044.11
208IL_47732.11
209IL_50911.1116S h34 ILa : Part of larger motif
210IL_92280.11
211IL_03110.11
212IL_02835.11
213IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
214IL_52958.11
215IL_06808.11Double sheared (tSH-tSH) one bulged base.
216IL_25314.11
217IL_20530.11
218IL_83856.11
219IL_76486.11Sarcin-ricin motif with syn G
220IL_57364.11LSU Helix 89 (H89) IL2
221IL_41139.11
222IL_06847.11Group II Intron IL
223IL_30354.11
224IL_85805.11
225IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
226IL_41791.11
227IL_06468.1116S h40 3WJ E.c.
228IL_80652.11
229IL_54450.11
230IL_13682.11
231IL_81398.11
232IL_97842.11
233IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
234IL_64589.11
235IL_54470.11tHS tHH bulge with S-turn
236IL_60649.11Kink-turn
237IL_46721.11
238IL_83250.1116S h40 3WJ T.th.
239IL_57977.11
240IL_39324.11
241IL_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.
242IL_12507.11
243IL_69799.11
244IL_47687.11
245IL_55649.11
246IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
247IL_37347.11
248IL_46306.11
249IL_82601.11Tandem cWW water-inserted CU pairs
250IL_91089.11
251IL_77296.11
252IL_41153.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.82441-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_73276.522C-loop
3IL_94403.43LSU H77

Removed motif groups

#Motif idInstancesDescription
1IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_10365.11
3IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW

Added motif groups

#Motif idInstancesDescription
1IL_39674.14LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_05513.11