Changes in PDB files used for clustering

Release 1.7 has 204 PDB files, release 1.8 has 206 PDB files, 204 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_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_92114.39GAAA loop receptor "platform" motif
27IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_90459.39cWW AG or UU
29IL_47444.39SRP Loop E-like motif
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_97057.36
34IL_25380.16LSU Helix 89 (H89) IL2
35IL_77263.26Kink-turn from U4
36IL_53635.36LSU Helix 32 (H32) IL
37IL_13069.36LSU 3WJ H32-H33-H35A
38IL_90133.36
39IL_72158.36LSU Helix 62 (H62) IL
40IL_08926.3623S H91 IL
41IL_70237.36
42IL_25230.36Bacterial 5S rRNA Loop E
43IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
44IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45IL_86357.35LSU Helix 61 IL2
46IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
47IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48IL_79083.35
49IL_25300.1516S h19 IL and 23S H41 IL
50IL_02359.35
51IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
52IL_21333.24tSH-tHW-bulge
53IL_34363.24Kink-turn from 23S H42
54IL_45262.44
55IL_39526.44
56IL_28572.2416S h18 kink-turn like motif
57IL_31066.34SSU Helix 44 (h44) extension
58IL_01080.14
59IL_39980.14
60IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62IL_22732.14tSH-inserted-tHS
63IL_98591.34
64IL_82188.24LSU H68 IL from H.m.
65IL_42251.14
66IL_38807.34
67IL_31663.1423S H73 ILa : Part of larger Motif
68IL_09530.14Double S-turn motif
69IL_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)
70IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
71IL_16166.4323S H91 IL
72IL_07300.23
73IL_52173.13
74IL_80348.1323S H91 IL
75IL_58586.23
76IL_43946.13
77IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
78IL_48918.23Kink-turn variant
79IL_98421.43SSU Helix 12 (h12) IL
80IL_05723.13
81IL_06211.13
82IL_79955.23SSU Helix (23) h23 IL1
83IL_95150.43
84IL_75447.13
85IL_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.
86IL_06180.13tHS tHH bulge with S-turn
87IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
88IL_80494.23LSU H58 IL2 H.m.
89IL_82563.13Thi-box riboswitch T-loop
90IL_87065.1323S H91 IL | Single-Base Intercalation Site
91IL_34628.23Kink-turn
92IL_30840.23
93IL_62499.73
94IL_37053.13Kink-turn from 23S H58
95IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
96IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
97IL_46034.12
98IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
99IL_97833.12
100IL_98566.12
101IL_12211.12
102IL_21495.12
103IL_37406.12
104IL_21639.12
105IL_76095.32Motif from Hairpin Ribozyme
106IL_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)
107IL_01054.12
108IL_15840.22Triple Sheared with unpaired, inserted A
109IL_94744.12Sarcin-ricin motif with extra cWW GA pair
110IL_97509.12Double sheared with wobble cWW.
111IL_37197.12
112IL_96446.12
113IL_31707.12Vitamin B12 aptamer
114IL_23262.42
115IL_69536.12LSU Helix 96 (H96) IL2
116IL_80433.12
117IL_45794.12
118IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
119IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
120IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
121IL_16330.12
122IL_87507.12tHS tHH bulge with S-turn
123IL_50521.12
124IL_09882.12
125IL_77076.12
126IL_80093.12
127IL_30381.12tHS tHH bulge with S-turn
128IL_23414.12
129IL_90735.12
130IL_40892.12
131IL_33964.12
132IL_87548.12
133IL_52940.12
134IL_90057.12
135IL_00998.12
136IL_11751.12
137IL_65137.12Kink-turn like motif in Group I Intron
138IL_19898.12
139IL_96206.12
140IL_46435.12
141IL_09587.12
142IL_67887.12
143IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
144IL_86059.11
145IL_43316.11
146IL_12507.11
147IL_06468.1116S h40 3WJ E.c.
148IL_52958.11
149IL_06808.11Double sheared (tSH-tSH) one bulged base.
150IL_77014.11
151IL_03741.11
152IL_88119.11
153IL_98924.11
154IL_59529.11
155IL_91904.11
156IL_21421.11
157IL_85510.11
158IL_49527.11
159IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
160IL_47732.11
161IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
162IL_40845.11
163IL_88865.11
164IL_80505.11
165IL_69799.11
166IL_47687.11
167IL_80652.11
168IL_54450.11
169IL_71942.11
170IL_91078.11
171IL_71685.11Sarcin-like with an intercalated basepair
172IL_25181.11
173IL_09491.11
174IL_58454.11
175IL_88367.11
176IL_49976.11
177IL_57285.11
178IL_30354.11
179IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
180IL_06177.11cWW AG or UU
181IL_82650.11
182IL_31006.11tSH-tHW-L-bif-cWW
183IL_55649.11
184IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
185IL_75328.11
186IL_06306.11
187IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
188IL_23639.11tWH-tHS-L-cWW
189IL_02957.11
190IL_18675.11cWW-bulge-cWW
191IL_40527.11Kink-turn
192IL_23448.11
193IL_46721.11
194IL_50911.1116S h34 ILa : Part of larger motif
195IL_92280.11
196IL_25307.11
197IL_26868.11
198IL_27243.11
199IL_25314.11
200IL_20530.11
201IL_83856.11
202IL_76486.11Sarcin-ricin motif with syn G
203IL_57364.11LSU Helix 89 (H89) IL2
204IL_41139.11
205IL_91044.11
206IL_27668.11
207IL_41153.11
208IL_85805.11
209IL_03110.11
210IL_02835.11
211IL_76263.11
212IL_91379.11
213IL_11302.11
214IL_89794.11
215IL_28644.11
216IL_52509.11
217IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
218IL_13682.11
219IL_81398.11
220IL_97842.11
221IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
222IL_64589.11
223IL_54470.11tHS tHH bulge with S-turn
224IL_06847.11Group II Intron IL
225IL_30067.11
226IL_83250.1116S h40 3WJ T.th.
227IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
228IL_41791.11
229IL_68827.11Reverse Kink-Turn
230IL_66744.11SSU Helix 21 (h21) IL2 E.coli
231IL_53988.11
232IL_61730.11
233IL_37347.11
234IL_46306.11
235IL_82601.11Tandem cWW water-inserted CU pairs
236IL_91089.11
237IL_60649.11Kink-turn
238IL_52610.11
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_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
243IL_83920.11
244IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
245IL_11778.11
246IL_75415.11Pseudo-knot forming internal loop
247IL_31224.1123S H91 IL
248IL_05221.11
249IL_06471.11
250IL_68767.11
251IL_17603.11
252IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
253IL_87523.11
254IL_77296.11
255IL_87394.11
256IL_63952.11
257IL_06421.11Single sheared with bulged bases
258IL_20775.11tSH-inserted
259IL_25082.11
260IL_53323.11
261IL_26971.11
262IL_56513.11
263IL_15205.11
264IL_21077.11
265IL_03282.11
266IL_42891.11

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