Changes in PDB files used for clustering

Release 0.10 has 195 PDB files, release 0.11 has 196 PDB files, 194 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 0.11: 3ZD3, 4E59.

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 0.10 has 266 motif groups, release 0.11 has 266 motif groups, 252 of them are identical.

6 motif groups were updated, 8 groups are present only in release 0.10, 8 groups are only in release 0.11.

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_39199.255Hoogsteen-edge Platform, Single bulged base
3IL_41766.249Tandem cWW pairs (Not AU or GC)
4IL_56465.245Single, unpaired intercalated base, consensus A
5IL_44540.243Sugar-edge, 1-base platform, consensus tHS
6IL_87904.331Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_06390.125cWH basepair with syn base
8IL_13959.224Double Sheared (tSH-tHS)
9IL_65553.422Kink-turn
10IL_93424.222tSH-inserted-tHW
11IL_32390.22116S h19 IL and 23S H41 IL
12IL_73276.120C-loop
13IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.21716S h21 S8 binding site
15IL_06429.216cWW-bulge-cWW
16IL_85647.216Sarcin-ricin parent motif with 15 Nts
17IL_94430.31516S h32-h33-h34 3WJ
18IL_31555.315Tandem sheared with inserted, unpaired purine.
19IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
20IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_40090.21116S h34 ILa : Part of larger motif
23IL_46648.11123S H91 IL | Single-Base Intercalation Site
24IL_27618.21123S H73 ILa : Part of larger Motif
25IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_58291.29Recurrent Sub-motif found in junctions
27IL_92114.39GAAA loop receptor "platform" motif
28IL_47444.39SRP Loop E-like motif
29IL_90459.28cWW AG or UU
30IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_73000.27cHS-cWS
34IL_86357.27LSU Helix 61 IL2
35IL_72158.26LSU Helix 62 (H62) IL
36IL_25230.26Bacterial 5S rRNA Loop E
37IL_70237.36
38IL_53635.26LSU Helix 32 (H32) IL
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_24022.26
41IL_10007.16Single sheared with bulged bases
42IL_54420.16
43IL_89088.1616S h19 IL and 23S H41 IL
44IL_97057.26
45IL_08926.1623S H91 IL
46IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_79083.25
48IL_45262.25
49IL_82188.15LSU H68 IL from H.m.
50IL_90133.15
51IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
52IL_77263.15Kink-turn from U4
53IL_01239.15
54IL_02359.25
55IL_78732.35Double S-turn motif
56IL_92484.15
57IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
58IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
59IL_38807.24
60IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
61IL_31066.24SSU Helix 44 (h44) extension
62IL_10005.14
63IL_21333.14tSH-tHW-bulge
64IL_39526.34
65IL_98591.24
66IL_22732.14tSH-inserted-tHS
67IL_28572.1416S h18 kink-turn like motif
68IL_16166.23
69IL_23262.33
70IL_34363.13Kink-turn from 23S H42
71IL_09348.33cWW-L-cWW-cWW
72IL_16252.2323S H91 IL
73IL_30840.13
74IL_34628.23Kink-turn
75IL_79955.23SSU Helix (23) h23 IL1
76IL_36254.13
77IL_82563.13Thi-box riboswitch T-loop
78IL_37053.13Kink-turn from 23S H58
79IL_53774.13Single sheared with bulged bases
80IL_58586.23
81IL_80494.23LSU H58 IL2 H.m.
82IL_95150.33
83IL_98421.23SSU Helix 12 (h12) IL
84IL_52173.13
85IL_71565.13
86IL_75447.13
87IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
88IL_43946.13
89IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
90IL_81441.12
91IL_91132.12
92IL_12211.12
93IL_28942.12
94IL_40892.12
95IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
96IL_69901.12
97IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
98IL_90057.12
99IL_23414.12
100IL_55287.12
101IL_77076.12
102IL_87548.12
103IL_94744.12Sarcin-ricin motif with extra cWW GA pair
104IL_97833.12
105IL_00998.12
106IL_09882.12
107IL_16330.12
108IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
109IL_41397.22LSU Helix 96 (H96) IL2
110IL_45794.12
111IL_70280.12Double sheared with wobble cWW.
112IL_74876.12
113IL_80093.12
114IL_01054.12
115IL_16377.12
116IL_50521.12
117IL_65137.12Kink-turn like motif in Group I Intron
118IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
119IL_37197.12
120IL_46435.12
121IL_98566.12
122IL_21495.12
123IL_31707.12Vitamin B12 aptamer
124IL_82831.22Kink-turn from 16S H23
125IL_07300.12
126IL_11751.12
127IL_37406.12
128IL_52940.12
129IL_76095.32Motif from Hairpin Ribozyme
130IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
131IL_89231.12LSU H77
132IL_15840.22Triple Sheared with unpaired, inserted A
133IL_25174.12
134IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
135IL_61730.11
136IL_67735.11
137IL_76256.11
138IL_78809.11
139IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
140IL_89794.11
141IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
142IL_98688.11
143IL_02835.11
144IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
145IL_20775.11tSH-inserted
146IL_25181.11
147IL_37990.11
148IL_53323.11
149IL_57977.11
150IL_61991.11
151IL_76486.11Sarcin-ricin motif with syn G
152IL_82113.11
153IL_83856.11
154IL_91904.11
155IL_98924.11
156IL_02957.11
157IL_12486.11
158IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
159IL_41139.11
160IL_47968.11
161IL_53423.11
162IL_83920.11
163IL_03110.11
164IL_06468.1116S h40 3WJ E.c.
165IL_12507.11
166IL_23639.11tWH-tHS-L-cWW
167IL_55649.11
168IL_58454.11
169IL_63952.11
170IL_77195.11
171IL_85510.11
172IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
173IL_97842.11
174IL_03282.11
175IL_06471.11
176IL_25307.11
177IL_31241.11
178IL_39324.11
179IL_46306.11
180IL_55934.11kink-turn-like
181IL_75415.11Pseudo-knot forming internal loop
182IL_82601.11Tandem cWW water-inserted CU pairs
183IL_88367.11
184IL_90880.11
185IL_92280.11
186IL_03741.11
187IL_06808.11Double sheared (tSH-tSH) one bulged base.
188IL_13682.11
189IL_21421.11
190IL_26868.11
191IL_41791.11
192IL_53988.11
193IL_59529.11
194IL_77296.11
195IL_80505.11
196IL_82650.11
197IL_85805.11
198IL_88403.11
199IL_91044.11
200IL_05221.11
201IL_06847.11Group II Intron IL
202IL_11302.11
203IL_17603.11
204IL_26971.11
205IL_37347.11
206IL_43316.11
207IL_52509.11
208IL_60643.11
209IL_65788.11
210IL_71685.11Sarcin-like with an intercalated basepair
211IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
212IL_80652.11
213IL_86059.11
214IL_91078.11
215IL_02690.11
216IL_05462.11
217IL_15205.11
218IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
219IL_22579.11
220IL_25082.11
221IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
222IL_40527.11Kink-turn
223IL_54450.11
224IL_56513.11
225IL_60649.11Kink-turn
226IL_66744.11SSU Helix 21 (h21) IL2 E.coli
227IL_71942.11
228IL_81398.11
229IL_83250.1116S h40 3WJ T.th.
230IL_91089.11
231IL_97073.11
232IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
233IL_06306.11
234IL_11869.11
235IL_18755.11
236IL_37715.11
237IL_40845.11
238IL_47687.11
239IL_52958.11
240IL_54576.11

Updated motif groups

#Motif idInstancesDescription
1IL_47174.5203cWW AG or water inserted cWW Y-Y.
2IL_40387.44LSU Helix 89 (H89) IL2
3IL_98556.34
4IL_34156.43cWW AG or UU
5IL_62499.43
6IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena

Removed motif groups

#Motif idInstancesDescription
1IL_86826.13tHS tHH bulge with S-turn
2IL_37737.12
3IL_73816.12tHS tHH bulge with S-turn
4IL_93782.12
5IL_06780.11
6IL_17268.11
7IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
8IL_70550.11

Added motif groups

#Motif idInstancesDescription
1IL_91547.13tHS tHH bulge with S-turn
2IL_33965.12tHS tHH bulge with S-turn
3IL_58811.12
4IL_37150.11tHS tHH bulge with S-turn
5IL_41864.11Part of H71 junction in 23S rRNA from T.th.
6IL_87544.11
7IL_96031.11tHS tHH bulge with S-turn
8IL_97961.11