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

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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_85647.316Sarcin-ricin parent motif with 15 Nts
15IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_94430.51616S h32-h33-h34 3WJ
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_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
24IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
25IL_58291.410Recurrent Sub-motif found in junctions
26IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_47444.39SRP Loop E-like motif
28IL_90459.39cWW AG or UU
29IL_92114.39GAAA loop receptor "platform" motif
30IL_73000.27cHS-cWS
31IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_13069.36LSU 3WJ H32-H33-H35A
34IL_53635.36LSU Helix 32 (H32) IL
35IL_90133.36
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_72158.36LSU Helix 62 (H62) IL
38IL_77263.26Kink-turn from U4
39IL_08926.3623S H91 IL
40IL_25380.16LSU Helix 89 (H89) IL2
41IL_97057.36
42IL_25230.36Bacterial 5S rRNA Loop E
43IL_70237.36
44IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
45IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
46IL_25300.1516S h19 IL and 23S H41 IL
47IL_86357.35LSU Helix 61 IL2
48IL_79083.35
49IL_02359.35
50IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
51IL_09530.14Double S-turn motif
52IL_31663.1423S H73 ILa : Part of larger Motif
53IL_39526.44
54IL_45262.44
55IL_21333.24tSH-tHW-bulge
56IL_39980.14
57IL_42251.14
58IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
59IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_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)
61IL_34363.24Kink-turn from 23S H42
62IL_38807.34
63IL_98591.34
64IL_01080.14
65IL_31066.34SSU Helix 44 (h44) extension
66IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67IL_22732.14tSH-inserted-tHS
68IL_28572.2416S h18 kink-turn like motif
69IL_82188.24LSU H68 IL from H.m.
70IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
71IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
72IL_37053.13Kink-turn from 23S H58
73IL_05723.13
74IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
75IL_80348.1323S H91 IL
76IL_82563.13Thi-box riboswitch T-loop
77IL_95150.43
78IL_06180.13tHS tHH bulge with S-turn
79IL_07300.23
80IL_52173.13
81IL_80494.23LSU H58 IL2 H.m.
82IL_98421.43SSU Helix 12 (h12) IL
83IL_06211.13
84IL_62499.73
85IL_30840.23
86IL_48918.23Kink-turn variant
87IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
88IL_34628.23Kink-turn
89IL_43946.13
90IL_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.
91IL_16166.4323S H91 IL
92IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
93IL_58586.23
94IL_75447.13
95IL_79955.23SSU Helix (23) h23 IL1
96IL_87065.1323S H91 IL | Single-Base Intercalation Site
97IL_16330.12
98IL_23262.42
99IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
100IL_76095.32Motif from Hairpin Ribozyme
101IL_80093.12
102IL_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)
103IL_87507.12tHS tHH bulge with S-turn
104IL_90057.12
105IL_94744.12Sarcin-ricin motif with extra cWW GA pair
106IL_97509.12Double sheared with wobble cWW.
107IL_23414.12
108IL_50521.12
109IL_97833.12
110IL_09587.12
111IL_31707.12Vitamin B12 aptamer
112IL_37197.12
113IL_45794.12
114IL_67887.12
115IL_77076.12
116IL_80433.12
117IL_87548.12
118IL_09882.12
119IL_46034.12
120IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
121IL_90735.12
122IL_00998.12
123IL_30381.12tHS tHH bulge with S-turn
124IL_33964.12
125IL_37406.12
126IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
127IL_98566.12
128IL_01054.12
129IL_11751.12
130IL_21495.12
131IL_46435.12
132IL_69536.12LSU Helix 96 (H96) IL2
133IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
134IL_96206.12
135IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
136IL_15840.22Triple Sheared with unpaired, inserted A
137IL_19898.12
138IL_21639.12
139IL_40892.12
140IL_52940.12
141IL_12211.12
142IL_65137.12Kink-turn like motif in Group I Intron
143IL_06471.11
144IL_12507.11
145IL_20775.11tSH-inserted
146IL_28644.11
147IL_41153.11
148IL_49976.11
149IL_53323.11
150IL_59529.11
151IL_02835.11
152IL_06808.11Double sheared (tSH-tSH) one bulged base.
153IL_21077.11
154IL_56513.11
155IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
156IL_66744.11SSU Helix 21 (h21) IL2 E.coli
157IL_71685.11Sarcin-like with an intercalated basepair
158IL_76486.11Sarcin-ricin motif with syn G
159IL_85510.11
160IL_87523.11
161IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
162IL_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.
163IL_06177.11cWW AG or UU
164IL_06847.11Group II Intron IL
165IL_13682.11
166IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
167IL_23639.11tWH-tHS-L-cWW
168IL_25307.11
169IL_30067.11
170IL_41791.11
171IL_47687.11
172IL_50911.1116S h34 ILa : Part of larger motif
173IL_53988.11
174IL_57364.11LSU Helix 89 (H89) IL2
175IL_60649.11Kink-turn
176IL_71942.11
177IL_82601.11Tandem cWW water-inserted CU pairs
178IL_97842.11
179IL_02957.11
180IL_17603.11
181IL_25314.11
182IL_30354.11
183IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
184IL_37347.11
185IL_47732.11
186IL_54450.11
187IL_61730.11
188IL_68767.11
189IL_82650.11
190IL_85805.11
191IL_92280.11
192IL_03110.11
193IL_11302.11
194IL_15205.11
195IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
196IL_21421.11
197IL_40527.11Kink-turn
198IL_46306.11
199IL_52509.11
200IL_54470.11tHS tHH bulge with S-turn
201IL_57977.11
202IL_77296.11
203IL_80505.11
204IL_83250.1116S h40 3WJ T.th.
205IL_86059.11
206IL_88119.11
207IL_91044.11
208IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
209IL_03282.11
210IL_06306.11
211IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
212IL_18675.11cWW-bulge-cWW
213IL_25082.11
214IL_26868.11
215IL_40845.11
216IL_43316.11
217IL_52610.11
218IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
219IL_63952.11
220IL_80652.11
221IL_88367.11
222IL_91078.11
223IL_03741.11
224IL_06421.11Single sheared with bulged bases
225IL_11778.11
226IL_25181.11
227IL_26971.11
228IL_55649.11
229IL_58454.11
230IL_64589.11
231IL_69799.11
232IL_75415.11Pseudo-knot forming internal loop
233IL_81398.11
234IL_83856.11
235IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
236IL_91089.11
237IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
238IL_05221.11
239IL_06468.1116S h40 3WJ E.c.
240IL_09491.11
241IL_20530.11
242IL_31224.1123S H91 IL
243IL_39324.11
244IL_41139.11
245IL_46721.11
246IL_49527.11
247IL_52958.11
248IL_83920.11
249IL_89794.11
250IL_91904.11
251IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
252IL_98924.11

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