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_93424.421tSH-inserted-tHW
11IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
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_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
21IL_46648.41123S H91 IL | Single-Base Intercalation Site
22IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_90459.39cWW AG or UU
28IL_47444.39SRP Loop E-like motif
29IL_92114.39GAAA loop receptor "platform" motif
30IL_73000.27cHS-cWS
31IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
32IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_25380.16LSU Helix 89 (H89) IL2
34IL_70237.36
35IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_97057.36
38IL_53635.36LSU Helix 32 (H32) IL
39IL_77263.26Kink-turn from U4
40IL_13069.36LSU 3WJ H32-H33-H35A
41IL_90133.36
42IL_72158.36LSU Helix 62 (H62) IL
43IL_08926.3623S H91 IL
44IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
45IL_25300.1516S h19 IL and 23S H41 IL
46IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
47IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
48IL_86357.35LSU Helix 61 IL2
49IL_79083.35
50IL_02359.35
51IL_98591.34
52IL_09530.14Double S-turn motif
53IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
54IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
55IL_22732.14tSH-inserted-tHS
56IL_82188.24LSU H68 IL from H.m.
57IL_39526.44
58IL_42251.14
59IL_38807.34
60IL_31663.1423S H73 ILa : Part of larger Motif
61IL_34363.24Kink-turn from 23S H42
62IL_45262.44
63IL_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)
64IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
65IL_21333.24tSH-tHW-bulge
66IL_28572.2416S h18 kink-turn like motif
67IL_31066.34SSU Helix 44 (h44) extension
68IL_01080.14
69IL_39980.14
70IL_80348.1323S H91 IL
71IL_05723.13
72IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
73IL_48918.23Kink-turn variant
74IL_98421.43SSU Helix 12 (h12) IL
75IL_06211.13
76IL_79955.23SSU Helix (23) h23 IL1
77IL_95150.43
78IL_80494.23LSU H58 IL2 H.m.
79IL_06180.13tHS tHH bulge with S-turn
80IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
81IL_37053.13Kink-turn from 23S H58
82IL_30840.23
83IL_62499.73
84IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
85IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
86IL_16166.4323S H91 IL
87IL_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.
88IL_34628.23Kink-turn
89IL_75447.13
90IL_87065.1323S H91 IL | Single-Base Intercalation Site
91IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
92IL_07300.23
93IL_52173.13
94IL_58586.23
95IL_43946.13
96IL_82563.13Thi-box riboswitch T-loop
97IL_31707.12Vitamin B12 aptamer
98IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
99IL_09587.12
100IL_80433.12
101IL_45794.12
102IL_80093.12
103IL_46435.12
104IL_37406.12
105IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
106IL_16330.12
107IL_87507.12tHS tHH bulge with S-turn
108IL_50521.12
109IL_09882.12
110IL_77076.12
111IL_21495.12
112IL_94744.12Sarcin-ricin motif with extra cWW GA pair
113IL_23414.12
114IL_90735.12
115IL_40892.12
116IL_33964.12
117IL_87548.12
118IL_52940.12
119IL_90057.12
120IL_96206.12
121IL_01054.12
122IL_15840.22Triple Sheared with unpaired, inserted A
123IL_23262.42
124IL_69536.12LSU Helix 96 (H96) IL2
125IL_11751.12
126IL_65137.12Kink-turn like motif in Group I Intron
127IL_19898.12
128IL_67887.12
129IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
130IL_98566.12
131IL_12211.12
132IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
133IL_46034.12
134IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
135IL_97833.12
136IL_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)
137IL_30381.12tHS tHH bulge with S-turn
138IL_00998.12
139IL_21639.12
140IL_76095.32Motif from Hairpin Ribozyme
141IL_97509.12Double sheared with wobble cWW.
142IL_37197.12
143IL_50911.1116S h34 ILa : Part of larger motif
144IL_92280.11
145IL_03110.11
146IL_02835.11
147IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
148IL_52958.11
149IL_06808.11Double sheared (tSH-tSH) one bulged base.
150IL_25314.11
151IL_20530.11
152IL_83856.11
153IL_76486.11Sarcin-ricin motif with syn G
154IL_57364.11LSU Helix 89 (H89) IL2
155IL_41139.11
156IL_06847.11Group II Intron IL
157IL_30354.11
158IL_85805.11
159IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
160IL_41791.11
161IL_06468.1116S h40 3WJ E.c.
162IL_80652.11
163IL_54450.11
164IL_13682.11
165IL_81398.11
166IL_97842.11
167IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
168IL_64589.11
169IL_54470.11tHS tHH bulge with S-turn
170IL_60649.11Kink-turn
171IL_46721.11
172IL_83250.1116S h40 3WJ T.th.
173IL_57977.11
174IL_39324.11
175IL_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.
176IL_12507.11
177IL_69799.11
178IL_47687.11
179IL_55649.11
180IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
181IL_37347.11
182IL_46306.11
183IL_82601.11Tandem cWW water-inserted CU pairs
184IL_91089.11
185IL_77296.11
186IL_41153.11
187IL_80505.11
188IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
189IL_75415.11Pseudo-knot forming internal loop
190IL_31224.1123S H91 IL
191IL_05221.11
192IL_06471.11
193IL_68767.11
194IL_17603.11
195IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
196IL_87523.11
197IL_03282.11
198IL_63952.11
199IL_86059.11
200IL_43316.11
201IL_82650.11
202IL_26868.11
203IL_89794.11
204IL_28644.11
205IL_52509.11
206IL_61730.11
207IL_25082.11
208IL_53323.11
209IL_26971.11
210IL_56513.11
211IL_15205.11
212IL_21077.11
213IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
214IL_25307.11
215IL_11302.11
216IL_53988.11
217IL_03741.11
218IL_88119.11
219IL_98924.11
220IL_59529.11
221IL_91904.11
222IL_21421.11
223IL_85510.11
224IL_49527.11
225IL_30067.11
226IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
227IL_40845.11
228IL_06177.11cWW AG or UU
229IL_66744.11SSU Helix 21 (h21) IL2 E.coli
230IL_11778.11
231IL_91078.11
232IL_71685.11Sarcin-like with an intercalated basepair
233IL_25181.11
234IL_09491.11
235IL_58454.11
236IL_88367.11
237IL_49976.11
238IL_52610.11
239IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
240IL_83920.11
241IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
242IL_06421.11Single sheared with bulged bases
243IL_20775.11tSH-inserted
244IL_71942.11
245IL_06306.11
246IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
247IL_23639.11tWH-tHS-L-cWW
248IL_02957.11
249IL_18675.11cWW-bulge-cWW
250IL_40527.11Kink-turn
251IL_91044.11
252IL_47732.11

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_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_10365.11

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