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_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_46648.41123S H91 IL | Single-Base Intercalation Site
21IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
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_90459.39cWW AG or UU
27IL_47444.39SRP Loop E-like motif
28IL_92114.39GAAA loop receptor "platform" motif
29IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
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_70237.36
34IL_25230.36Bacterial 5S rRNA Loop E
35IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36IL_97057.36
37IL_25380.16LSU Helix 89 (H89) IL2
38IL_77263.26Kink-turn from U4
39IL_53635.36LSU Helix 32 (H32) IL
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_79083.35
46IL_25300.1516S h19 IL and 23S H41 IL
47IL_02359.35
48IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
49IL_86357.35LSU Helix 61 IL2
50IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
51IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
52IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
53IL_22732.14tSH-inserted-tHS
54IL_98591.34
55IL_82188.24LSU H68 IL from H.m.
56IL_42251.14
57IL_38807.34
58IL_31663.1423S H73 ILa : Part of larger Motif
59IL_09530.14Double S-turn motif
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_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
62IL_21333.24tSH-tHW-bulge
63IL_34363.24Kink-turn from 23S H42
64IL_45262.44
65IL_39526.44
66IL_28572.2416S h18 kink-turn like motif
67IL_31066.34SSU Helix 44 (h44) extension
68IL_01080.14
69IL_39980.14
70IL_98421.43SSU Helix 12 (h12) IL
71IL_05723.13
72IL_06211.13
73IL_79955.23SSU Helix (23) h23 IL1
74IL_95150.43
75IL_75447.13
76IL_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.
77IL_06180.13tHS tHH bulge with S-turn
78IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
79IL_80494.23LSU H58 IL2 H.m.
80IL_82563.13Thi-box riboswitch T-loop
81IL_87065.1323S H91 IL | Single-Base Intercalation Site
82IL_34628.23Kink-turn
83IL_30840.23
84IL_62499.73
85IL_37053.13Kink-turn from 23S H58
86IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
87IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
88IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
89IL_16166.4323S H91 IL
90IL_07300.23
91IL_52173.13
92IL_80348.1323S H91 IL
93IL_58586.23
94IL_43946.13
95IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
96IL_48918.23Kink-turn variant
97IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
98IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
99IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
100IL_16330.12
101IL_87507.12tHS tHH bulge with S-turn
102IL_50521.12
103IL_09882.12
104IL_77076.12
105IL_80093.12
106IL_30381.12tHS tHH bulge with S-turn
107IL_23414.12
108IL_90735.12
109IL_40892.12
110IL_33964.12
111IL_87548.12
112IL_52940.12
113IL_90057.12
114IL_00998.12
115IL_11751.12
116IL_65137.12Kink-turn like motif in Group I Intron
117IL_19898.12
118IL_96206.12
119IL_46435.12
120IL_09587.12
121IL_67887.12
122IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
123IL_46034.12
124IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
125IL_97833.12
126IL_98566.12
127IL_12211.12
128IL_21495.12
129IL_37406.12
130IL_21639.12
131IL_76095.32Motif from Hairpin Ribozyme
132IL_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)
133IL_01054.12
134IL_15840.22Triple Sheared with unpaired, inserted A
135IL_94744.12Sarcin-ricin motif with extra cWW GA pair
136IL_97509.12Double sheared with wobble cWW.
137IL_37197.12
138IL_96446.12
139IL_31707.12Vitamin B12 aptamer
140IL_23262.42
141IL_69536.12LSU Helix 96 (H96) IL2
142IL_80433.12
143IL_45794.12
144IL_85805.11
145IL_03110.11
146IL_02835.11
147IL_76263.11
148IL_91379.11
149IL_11302.11
150IL_89794.11
151IL_28644.11
152IL_52509.11
153IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
154IL_13682.11
155IL_81398.11
156IL_97842.11
157IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
158IL_64589.11
159IL_54470.11tHS tHH bulge with S-turn
160IL_06847.11Group II Intron IL
161IL_30067.11
162IL_83250.1116S h40 3WJ T.th.
163IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
164IL_41791.11
165IL_68827.11Reverse Kink-Turn
166IL_66744.11SSU Helix 21 (h21) IL2 E.coli
167IL_53988.11
168IL_61730.11
169IL_37347.11
170IL_46306.11
171IL_82601.11Tandem cWW water-inserted CU pairs
172IL_91089.11
173IL_60649.11Kink-turn
174IL_52610.11
175IL_57977.11
176IL_39324.11
177IL_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.
178IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
179IL_83920.11
180IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
181IL_11778.11
182IL_75415.11Pseudo-knot forming internal loop
183IL_31224.1123S H91 IL
184IL_05221.11
185IL_06471.11
186IL_68767.11
187IL_17603.11
188IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
189IL_87523.11
190IL_77296.11
191IL_87394.11
192IL_63952.11
193IL_06421.11Single sheared with bulged bases
194IL_20775.11tSH-inserted
195IL_25082.11
196IL_53323.11
197IL_26971.11
198IL_56513.11
199IL_15205.11
200IL_21077.11
201IL_03282.11
202IL_42891.11
203IL_86059.11
204IL_43316.11
205IL_12507.11
206IL_06468.1116S h40 3WJ E.c.
207IL_52958.11
208IL_06808.11Double sheared (tSH-tSH) one bulged base.
209IL_77014.11
210IL_03741.11
211IL_88119.11
212IL_98924.11
213IL_59529.11
214IL_91904.11
215IL_21421.11
216IL_85510.11
217IL_49527.11
218IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
219IL_47732.11
220IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
221IL_40845.11
222IL_88865.11
223IL_80505.11
224IL_69799.11
225IL_47687.11
226IL_80652.11
227IL_54450.11
228IL_71942.11
229IL_91078.11
230IL_71685.11Sarcin-like with an intercalated basepair
231IL_25181.11
232IL_09491.11
233IL_58454.11
234IL_88367.11
235IL_49976.11
236IL_57285.11
237IL_30354.11
238IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
239IL_06177.11cWW AG or UU
240IL_82650.11
241IL_31006.11tSH-tHW-L-bif-cWW
242IL_55649.11
243IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
244IL_75328.11
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_23448.11
252IL_46721.11
253IL_50911.1116S h34 ILa : Part of larger motif
254IL_92280.11
255IL_25307.11
256IL_26868.11
257IL_27243.11
258IL_25314.11
259IL_20530.11
260IL_83856.11
261IL_76486.11Sarcin-ricin motif with syn G
262IL_57364.11LSU Helix 89 (H89) IL2
263IL_41139.11
264IL_91044.11
265IL_27668.11
266IL_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_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