Changes in PDB files used for clustering

Release 0.9 has 195 PDB files, release 0.10 has 195 PDB files, 193 of them are identical.

2 equivalence classes changed representatives: 3U4M3UMY, 3G784FAW.

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 0.9 has 264 motif groups, release 0.10 has 266 motif groups, 244 of them are identical.

8 motif groups were updated, 12 groups are present only in release 0.9, 14 groups are only in release 0.10.

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_39199.255Hoogsteen-edge Platform, Single bulged base
2IL_41766.249Tandem cWW pairs (Not AU or GC)
3IL_56465.245Single, unpaired intercalated base, consensus A
4IL_44540.243Sugar-edge, 1-base platform, consensus tHS
5IL_06390.125cWH basepair with syn base
6IL_13959.224Double Sheared (tSH-tHS)
7IL_93424.222tSH-inserted-tHW
8IL_32390.22116S h19 IL and 23S H41 IL
9IL_73276.120C-loop
10IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
11IL_92027.21716S h21 S8 binding site
12IL_85647.216Sarcin-ricin parent motif with 15 Nts
13IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
14IL_94430.31516S h32-h33-h34 3WJ
15IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
16IL_40090.21116S h34 ILa : Part of larger motif
17IL_46648.11123S H91 IL | Single-Base Intercalation Site
18IL_27618.21123S H73 ILa : Part of larger Motif
19IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
20IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
21IL_58291.29Recurrent Sub-motif found in junctions
22IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
23IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
24IL_90459.28cWW AG or UU
25IL_73000.27cHS-cWS
26IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
27IL_86357.27LSU Helix 61 IL2
28IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
29IL_53635.26LSU Helix 32 (H32) IL
30IL_72158.26LSU Helix 62 (H62) IL
31IL_89088.1616S h19 IL and 23S H41 IL
32IL_13069.26LSU 3WJ H32-H33-H35A
33IL_54420.16
34IL_24022.26
35IL_25230.26Bacterial 5S rRNA Loop E
36IL_10007.16Single sheared with bulged bases
37IL_70237.36
38IL_08926.1623S H91 IL
39IL_97057.26
40IL_90133.15
41IL_02359.25
42IL_92484.15
43IL_82188.15LSU H68 IL from H.m.
44IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
45IL_45262.25
46IL_79083.25
47IL_77263.15Kink-turn from U4
48IL_01239.15
49IL_78732.35Double S-turn motif
50IL_39526.34
51IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
52IL_22732.14tSH-inserted-tHS
53IL_98591.24
54IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
55IL_21333.14tSH-tHW-bulge
56IL_40387.34
57IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
58IL_38807.24
59IL_28572.1416S h18 kink-turn like motif
60IL_31066.24SSU Helix 44 (h44) extension
61IL_98556.24
62IL_98421.23SSU Helix 12 (h12) IL
63IL_30840.13
64IL_16166.23
65IL_71565.13
66IL_95150.33
67IL_79955.23SSU Helix (23) h23 IL1
68IL_58586.23
69IL_80494.23LSU H58 IL2 H.m.
70IL_62499.33
71IL_37053.13Kink-turn from 23S H58
72IL_23262.33
73IL_86826.13tHS tHH bulge with S-turn
74IL_09348.33cWW-L-cWW-cWW
75IL_16252.2323S H91 IL
76IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
77IL_52173.13
78IL_43946.13
79IL_75447.13
80IL_34363.13Kink-turn from 23S H42
81IL_36254.13
82IL_82563.13Thi-box riboswitch T-loop
83IL_89028.23Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
84IL_34628.23Kink-turn
85IL_53774.13Single sheared with bulged bases
86IL_31707.12Vitamin B12 aptamer
87IL_09882.12
88IL_46435.12
89IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
90IL_37737.12
91IL_93782.12
92IL_21495.12
93IL_25174.12
94IL_37197.12
95IL_50521.12
96IL_80093.12
97IL_37406.12
98IL_41397.22LSU Helix 96 (H96) IL2
99IL_70280.12Double sheared with wobble cWW.
100IL_94744.12Sarcin-ricin motif with extra cWW GA pair
101IL_55287.12
102IL_45794.12
103IL_87548.12
104IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
105IL_52940.12
106IL_65137.12Kink-turn like motif in Group I Intron
107IL_97833.12
108IL_12211.12
109IL_01054.12
110IL_15840.22Triple Sheared with unpaired, inserted A
111IL_07300.12
112IL_16330.12
113IL_11751.12
114IL_76095.32Motif from Hairpin Ribozyme
115IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
116IL_34156.32cWW AG or UU
117IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
118IL_23414.12
119IL_40892.12
120IL_73816.12tHS tHH bulge with S-turn
121IL_81441.12
122IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
123IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
124IL_91132.12
125IL_28942.12
126IL_90057.12
127IL_98566.12
128IL_82831.22Kink-turn from 16S H23
129IL_00998.12
130IL_74876.12
131IL_88403.11
132IL_80652.11
133IL_12486.11
134IL_31241.11
135IL_76256.11
136IL_25082.11
137IL_71685.11Sarcin-like with an intercalated basepair
138IL_25181.11
139IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
140IL_60643.11
141IL_85805.11
142IL_02835.11
143IL_12507.11
144IL_06468.1116S h40 3WJ E.c.
145IL_52958.11
146IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
147IL_97073.11
148IL_54450.11
149IL_71942.11
150IL_53423.11
151IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
152IL_23639.11tWH-tHS-L-cWW
153IL_90880.11
154IL_15205.11
155IL_83250.1116S h40 3WJ T.th.
156IL_43316.11
157IL_80505.11
158IL_61991.11
159IL_47687.11
160IL_22579.11
161IL_67735.11
162IL_76486.11Sarcin-ricin motif with syn G
163IL_37990.11
164IL_17603.11
165IL_85510.11
166IL_03110.11
167IL_41791.11
168IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
169IL_82650.11
170IL_06780.11
171IL_55649.11
172IL_52509.11
173IL_37715.11
174IL_55934.11kink-turn-like
175IL_61730.11
176IL_13682.11
177IL_97842.11
178IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
179IL_56513.11
180IL_88367.11
181IL_63952.11
182IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
183IL_86059.11
184IL_25307.11
185IL_26868.11
186IL_78809.11
187IL_06306.11
188IL_37347.11
189IL_46306.11
190IL_21421.11
191IL_40527.11Kink-turn
192IL_92280.11
193IL_39324.11
194IL_11302.11
195IL_89794.11
196IL_65788.11
197IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
198IL_54576.11
199IL_75415.11Pseudo-knot forming internal loop
200IL_83856.11
201IL_05221.11
202IL_06471.11
203IL_58454.11
204IL_41139.11
205IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
206IL_40845.11
207IL_57977.11
208IL_98688.11
209IL_66744.11SSU Helix 21 (h21) IL2 E.coli
210IL_53988.11
211IL_20775.11tSH-inserted
212IL_11869.11
213IL_03741.11
214IL_81398.11
215IL_53323.11
216IL_26971.11
217IL_91904.11
218IL_18755.11
219IL_70550.11
220IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
221IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
222IL_83920.11
223IL_05462.11
224IL_06808.11Double sheared (tSH-tSH) one bulged base.
225IL_02690.11
226IL_91078.11
227IL_82113.11
228IL_98924.11
229IL_59529.11
230IL_02957.11
231IL_82601.11Tandem cWW water-inserted CU pairs
232IL_91089.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.42351-3 bulged nucleotides, same chain
2IL_47174.420216S h34 ILa : Part of larger motif
3IL_87904.331Triple sheared (tSH-tHS-tHS) no inserted bases
4IL_65553.422Kink-turn
5IL_06429.216cWW-bulge-cWW
6IL_31555.315Tandem sheared with inserted, unpaired purine.
7IL_47444.39SRP Loop E-like motif
8IL_92114.39GAAA loop receptor "platform" motif

Removed motif groups

Added motif groups

#Motif idInstancesDescription
1IL_10005.14
2IL_69901.12
3IL_77076.12
4IL_16377.12
5IL_89231.12LSU H77
6IL_03282.11
7IL_06847.11Group II Intron IL
8IL_77195.11
9IL_77296.11
10IL_17268.11
11IL_91044.11
12IL_47968.11
13IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
14IL_60649.11Kink-turn