Changes in PDB files used for clustering

Release 0.10 has 196 PDB files, release 0.11 has 197 PDB files, 195 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_93424.222tSH-inserted-tHW
10IL_65553.422Kink-turn
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_85647.216Sarcin-ricin parent motif with 15 Nts
16IL_06429.216cWW-bulge-cWW
17IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
18IL_94430.31516S h32-h33-h34 3WJ
19IL_31555.315Tandem sheared with inserted, unpaired purine.
20IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_27618.21123S H73 ILa : Part of larger Motif
22IL_40090.21116S h34 ILa : Part of larger motif
23IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_46648.11123S H91 IL | Single-Base Intercalation Site
25IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_47444.39SRP Loop E-like motif
27IL_92114.39GAAA loop receptor "platform" motif
28IL_58291.29Recurrent Sub-motif found in junctions
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_73000.27cHS-cWS
33IL_86357.27LSU Helix 61 IL2
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_70237.36
36IL_24022.26
37IL_54420.16
38IL_10007.16Single sheared with bulged bases
39IL_89088.1616S h19 IL and 23S H41 IL
40IL_08926.1623S H91 IL
41IL_25230.26Bacterial 5S rRNA Loop E
42IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43IL_97057.26
44IL_53635.26LSU Helix 32 (H32) IL
45IL_72158.26LSU Helix 62 (H62) IL
46IL_13069.26LSU 3WJ H32-H33-H35A
47IL_82188.15LSU H68 IL from H.m.
48IL_79083.25
49IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
50IL_45262.25
51IL_90133.15
52IL_78732.35Double S-turn motif
53IL_02359.25
54IL_77263.15Kink-turn from U4
55IL_01239.15
56IL_92484.15
57IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
58IL_10005.14
59IL_22732.14tSH-inserted-tHS
60IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
61IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62IL_38807.24
63IL_21333.14tSH-tHW-bulge
64IL_31066.24SSU Helix 44 (h44) extension
65IL_28572.1416S h18 kink-turn like motif
66IL_98591.24
67IL_39526.34
68IL_58586.23
69IL_09348.33cWW-L-cWW-cWW
70IL_98421.23SSU Helix 12 (h12) IL
71IL_80494.23LSU H58 IL2 H.m.
72IL_16252.2323S H91 IL
73IL_95150.33
74IL_37053.13Kink-turn from 23S H58
75IL_43946.13
76IL_23262.33
77IL_79955.23SSU Helix (23) h23 IL1
78IL_34363.13Kink-turn from 23S H42
79IL_36254.13
80IL_75447.13
81IL_30840.13
82IL_53774.13Single sheared with bulged bases
83IL_34628.23Kink-turn
84IL_16166.23
85IL_82563.13Thi-box riboswitch T-loop
86IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
87IL_52173.13
88IL_71565.13
89IL_31707.12Vitamin B12 aptamer
90IL_80093.12
91IL_21495.12
92IL_37406.12
93IL_89231.12LSU H77
94IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
95IL_12211.12
96IL_96446.12
97IL_09882.12
98IL_77076.12
99IL_01054.12
100IL_15840.22Triple Sheared with unpaired, inserted A
101IL_81441.12
102IL_55287.12
103IL_37197.12
104IL_50521.12
105IL_90057.12
106IL_91132.12
107IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
108IL_28942.12
109IL_07300.12
110IL_45794.12
111IL_87548.12
112IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
113IL_52940.12
114IL_65137.12Kink-turn like motif in Group I Intron
115IL_23414.12
116IL_16330.12
117IL_11751.12
118IL_97833.12
119IL_98566.12
120IL_00998.12
121IL_74876.12
122IL_40892.12
123IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
124IL_76095.32Motif from Hairpin Ribozyme
125IL_82831.22Kink-turn from 16S H23
126IL_41397.22LSU Helix 96 (H96) IL2
127IL_69901.12
128IL_25174.12
129IL_16377.12
130IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
131IL_46435.12
132IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
133IL_70280.12Double sheared with wobble cWW.
134IL_94744.12Sarcin-ricin motif with extra cWW GA pair
135IL_03110.11
136IL_43316.11
137IL_12507.11
138IL_06468.1116S h40 3WJ E.c.
139IL_37715.11
140IL_55934.11kink-turn-like
141IL_27243.11
142IL_71942.11
143IL_91078.11
144IL_25082.11
145IL_98924.11
146IL_59529.11
147IL_02957.11
148IL_82601.11Tandem cWW water-inserted CU pairs
149IL_23448.11
150IL_57285.11
151IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
152IL_41791.11
153IL_86059.11
154IL_80505.11
155IL_61991.11
156IL_47687.11
157IL_31006.11tSH-tHW-L-bif-cWW
158IL_55649.11
159IL_61730.11
160IL_75328.11
161IL_53423.11
162IL_77195.11
163IL_71685.11Sarcin-like with an intercalated basepair
164IL_25181.11
165IL_47968.11
166IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
167IL_60643.11
168IL_85805.11
169IL_39324.11
170IL_82650.11
171IL_20775.11tSH-inserted
172IL_65788.11
173IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
174IL_78809.11
175IL_67735.11
176IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
177IL_23639.11tWH-tHS-L-cWW
178IL_90880.11
179IL_15205.11
180IL_91044.11
181IL_27668.11
182IL_83250.1116S h40 3WJ T.th.
183IL_57977.11
184IL_76263.11
185IL_25307.11
186IL_26868.11
187IL_89794.11
188IL_05462.11
189IL_06808.11Double sheared (tSH-tSH) one bulged base.
190IL_11869.11
191IL_54576.11
192IL_13682.11
193IL_76486.11Sarcin-ricin motif with syn G
194IL_37990.11
195IL_17603.11
196IL_85510.11
197IL_06847.11Group II Intron IL
198IL_91379.11
199IL_11302.11
200IL_53988.11
201IL_80652.11
202IL_02690.11
203IL_06306.11
204IL_97842.11
205IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
206IL_56513.11
207IL_88367.11
208IL_60649.11Kink-turn
209IL_63952.11
210IL_68827.11Reverse Kink-Turn
211IL_98688.11
212IL_66744.11SSU Helix 21 (h21) IL2 E.coli
213IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
214IL_97073.11
215IL_12486.11
216IL_31241.11
217IL_75415.11Pseudo-knot forming internal loop
218IL_83856.11
219IL_37347.11
220IL_46306.11
221IL_21421.11
222IL_40527.11Kink-turn
223IL_77296.11
224IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
225IL_88865.11
226IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
227IL_83920.11
228IL_54450.11
229IL_76256.11
230IL_81398.11
231IL_05221.11
232IL_06471.11
233IL_58454.11
234IL_41139.11
235IL_03282.11
236IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
237IL_40845.11
238IL_92280.11
239IL_02835.11
240IL_88403.11
241IL_52958.11
242IL_52509.11
243IL_22579.11
244IL_77014.11
245IL_03741.11
246IL_82113.11
247IL_53323.11
248IL_26971.11
249IL_91904.11
250IL_18755.11
251IL_91089.11
252IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:

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_62499.43
5IL_89028.33Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
6IL_34156.43cWW AG or UU

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_17268.11
6IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
7IL_70550.11
8IL_06780.11

Added motif groups

#Motif idInstancesDescription
1IL_91547.13tHS tHH bulge with S-turn
2IL_58811.12
3IL_33965.12tHS tHH bulge with S-turn
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