Changes in PDB files used for clustering

Release 0.11 has 196 PDB files, release 0.12 has 196 PDB files, 196 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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 0.11 has 266 motif groups, release 0.12 has 266 motif groups, 266 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.11, 0 groups are only in release 0.12.

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_97217.42351-3 bulged nucleotides, same chain
2IL_47174.5203cWW AG or water inserted cWW Y-Y.
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.331Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_65553.422Kink-turn
11IL_93424.222tSH-inserted-tHW
12IL_32390.22116S h19 IL and 23S H41 IL
13IL_73276.120C-loop
14IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.21716S h21 S8 binding site
16IL_06429.216cWW-bulge-cWW
17IL_85647.216Sarcin-ricin parent motif with 15 Nts
18IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_94430.31516S h32-h33-h34 3WJ
20IL_31555.315Tandem sheared with inserted, unpaired purine.
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_46648.11123S H91 IL | Single-Base Intercalation Site
23IL_40090.21116S h34 ILa : Part of larger motif
24IL_27618.21123S H73 ILa : Part of larger Motif
25IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_92114.39GAAA loop receptor "platform" motif
28IL_58291.29Recurrent Sub-motif found in junctions
29IL_47444.39SRP Loop E-like motif
30IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_90459.28cWW AG or UU
33IL_73000.27cHS-cWS
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_86357.27LSU Helix 61 IL2
36IL_53635.26LSU Helix 32 (H32) IL
37IL_72158.26LSU Helix 62 (H62) IL
38IL_13069.26LSU 3WJ H32-H33-H35A
39IL_70237.36
40IL_24022.26
41IL_54420.16
42IL_25230.26Bacterial 5S rRNA Loop E
43IL_89088.1616S h19 IL and 23S H41 IL
44IL_10007.16Single sheared with bulged bases
45IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
46IL_97057.26
47IL_08926.1623S H91 IL
48IL_77263.15Kink-turn from U4
49IL_90133.15
50IL_01239.15
51IL_92484.15
52IL_02359.25
53IL_82188.15LSU H68 IL from H.m.
54IL_78732.35Double S-turn motif
55IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
56IL_45262.25
57IL_79083.25
58IL_28572.1416S h18 kink-turn like motif
59IL_31066.24SSU Helix 44 (h44) extension
60IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_10005.14
62IL_98591.24
63IL_40387.44LSU Helix 89 (H89) IL2
64IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
65IL_22732.14tSH-inserted-tHS
66IL_39526.34
67IL_98556.34
68IL_38807.24
69IL_21333.14tSH-tHW-bulge
70IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
71IL_36254.13
72IL_75447.13
73IL_52173.13
74IL_58586.23
75IL_82563.13Thi-box riboswitch T-loop
76IL_34628.23Kink-turn
77IL_98421.23SSU Helix 12 (h12) IL
78IL_71565.13
79IL_30840.13
80IL_53774.13Single sheared with bulged bases
81IL_95150.33
82IL_80494.23LSU H58 IL2 H.m.
83IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
84IL_79955.23SSU Helix (23) h23 IL1
85IL_37053.13Kink-turn from 23S H58
86IL_34156.43cWW AG or UU
87IL_23262.33
88IL_62499.43
89IL_34363.13Kink-turn from 23S H42
90IL_43946.13
91IL_09348.33cWW-L-cWW-cWW
92IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
93IL_16166.23
94IL_16252.2323S H91 IL
95IL_91547.13tHS tHH bulge with S-turn
96IL_76095.32Motif from Hairpin Ribozyme
97IL_00998.12
98IL_45794.12
99IL_31707.12Vitamin B12 aptamer
100IL_28942.12
101IL_16377.12
102IL_16330.12
103IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
104IL_80093.12
105IL_82831.22Kink-turn from 16S H23
106IL_74876.12
107IL_40892.12
108IL_58811.12
109IL_89231.12LSU H77
110IL_46435.12
111IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
112IL_33965.12tHS tHH bulge with S-turn
113IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
114IL_50521.12
115IL_09882.12
116IL_77076.12
117IL_12211.12
118IL_21495.12
119IL_37406.12
120IL_41397.22LSU Helix 96 (H96) IL2
121IL_69901.12
122IL_25174.12
123IL_87548.12
124IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
125IL_52940.12
126IL_90057.12
127IL_91132.12
128IL_70280.12Double sheared with wobble cWW.
129IL_94744.12Sarcin-ricin motif with extra cWW GA pair
130IL_55287.12
131IL_11751.12
132IL_65137.12Kink-turn like motif in Group I Intron
133IL_01054.12
134IL_15840.22Triple Sheared with unpaired, inserted A
135IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
136IL_97833.12
137IL_98566.12
138IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
139IL_81441.12
140IL_23414.12
141IL_07300.12
142IL_37197.12
143IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
144IL_40845.11
145IL_96031.11tHS tHH bulge with S-turn
146IL_11302.11
147IL_05462.11
148IL_20775.11tSH-inserted
149IL_65788.11
150IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
151IL_54576.11
152IL_75415.11Pseudo-knot forming internal loop
153IL_06306.11
154IL_76486.11Sarcin-ricin motif with syn G
155IL_37990.11
156IL_90880.11
157IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
158IL_60643.11
159IL_92280.11
160IL_02835.11
161IL_68827.11Reverse Kink-Turn
162IL_98688.11
163IL_66744.11SSU Helix 21 (h21) IL2 E.coli
164IL_06808.11Double sheared (tSH-tSH) one bulged base.
165IL_11869.11
166IL_83856.11
167IL_97842.11
168IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
169IL_17603.11
170IL_15205.11
171IL_91044.11
172IL_03110.11
173IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
174IL_83920.11
175IL_52958.11
176IL_80652.11
177IL_02690.11
178IL_03741.11
179IL_81398.11
180IL_37347.11
181IL_46306.11
182IL_41864.11Part of H71 junction in 23S rRNA from T.th.
183IL_06847.11Group II Intron IL
184IL_85805.11
185IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
186IL_41791.11
187IL_43316.11
188IL_88403.11
189IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
190IL_97073.11
191IL_12486.11
192IL_31241.11
193IL_76256.11
194IL_91078.11
195IL_82113.11
196IL_05221.11
197IL_06471.11
198IL_56513.11
199IL_85510.11
200IL_60649.11Kink-turn
201IL_83250.1116S h40 3WJ T.th.
202IL_57977.11
203IL_39324.11
204IL_86059.11
205IL_12507.11
206IL_06468.1116S h40 3WJ E.c.
207IL_54450.11
208IL_71942.11
209IL_87544.11
210IL_25082.11
211IL_53323.11
212IL_26971.11
213IL_91904.11
214IL_21421.11
215IL_88367.11
216IL_77296.11
217IL_80505.11
218IL_61991.11
219IL_47687.11
220IL_55649.11
221IL_52509.11
222IL_22579.11
223IL_53423.11
224IL_77195.11
225IL_98924.11
226IL_59529.11
227IL_02957.11
228IL_58454.11
229IL_40527.11Kink-turn
230IL_03282.11
231IL_63952.11
232IL_82650.11
233IL_89794.11
234IL_37150.11tHS tHH bulge with S-turn
235IL_37715.11
236IL_55934.11kink-turn-like
237IL_61730.11
238IL_13682.11
239IL_67735.11
240IL_97961.11
241IL_71685.11Sarcin-like with an intercalated basepair
242IL_25181.11
243IL_47968.11
244IL_18755.11
245IL_41139.11
246IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
247IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
248IL_76263.11
249IL_25307.11
250IL_26868.11
251IL_53988.11
252IL_78809.11
253IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
254IL_23639.11tWH-tHS-L-cWW
255IL_82601.11Tandem cWW water-inserted CU pairs
256IL_91089.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription