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_27618.21123S H73 ILa : Part of larger Motif
17IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
18IL_40090.21116S h34 ILa : Part of larger motif
19IL_46648.11123S H91 IL | Single-Base Intercalation Site
20IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
21IL_58291.29Recurrent Sub-motif found in junctions
22IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
23IL_90459.28cWW AG or UU
24IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
25IL_73000.27cHS-cWS
26IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
27IL_86357.27LSU Helix 61 IL2
28IL_54420.16
29IL_24022.26
30IL_25230.26Bacterial 5S rRNA Loop E
31IL_10007.16Single sheared with bulged bases
32IL_70237.36
33IL_08926.1623S H91 IL
34IL_97057.26
35IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36IL_53635.26LSU Helix 32 (H32) IL
37IL_72158.26LSU Helix 62 (H62) IL
38IL_89088.1616S h19 IL and 23S H41 IL
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_92484.15
41IL_82188.15LSU H68 IL from H.m.
42IL_02359.25
43IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
44IL_45262.25
45IL_77263.15Kink-turn from U4
46IL_01239.15
47IL_79083.25
48IL_90133.15
49IL_78732.35Double S-turn motif
50IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
51IL_21333.14tSH-tHW-bulge
52IL_39526.34
53IL_40387.34
54IL_38807.24
55IL_28572.1416S h18 kink-turn like motif
56IL_31066.24SSU Helix 44 (h44) extension
57IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
58IL_98556.24
59IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60IL_22732.14tSH-inserted-tHS
61IL_98591.24
62IL_95150.33
63IL_79955.23SSU Helix (23) h23 IL1
64IL_30840.13
65IL_58586.23
66IL_80494.23LSU H58 IL2 H.m.
67IL_62499.33
68IL_37053.13Kink-turn from 23S H58
69IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
70IL_52173.13
71IL_43946.13
72IL_34363.13Kink-turn from 23S H42
73IL_23262.33
74IL_86826.13tHS tHH bulge with S-turn
75IL_09348.33cWW-L-cWW-cWW
76IL_16252.2323S H91 IL
77IL_36254.13
78IL_75447.13
79IL_98421.23SSU Helix 12 (h12) IL
80IL_82563.13Thi-box riboswitch T-loop
81IL_89028.23Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
82IL_34628.23Kink-turn
83IL_16166.23
84IL_71565.13
85IL_53774.13Single sheared with bulged bases
86IL_50521.12
87IL_80093.12
88IL_46435.12
89IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
90IL_37737.12
91IL_93782.12
92IL_87548.12
93IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
94IL_52940.12
95IL_65137.12Kink-turn like motif in Group I Intron
96IL_97833.12
97IL_12211.12
98IL_21495.12
99IL_25174.12
100IL_37197.12
101IL_11751.12
102IL_76095.32Motif from Hairpin Ribozyme
103IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
104IL_34156.32cWW AG or UU
105IL_37406.12
106IL_41397.22LSU Helix 96 (H96) IL2
107IL_70280.12Double sheared with wobble cWW.
108IL_94744.12Sarcin-ricin motif with extra cWW GA pair
109IL_55287.12
110IL_45794.12
111IL_01054.12
112IL_15840.22Triple Sheared with unpaired, inserted A
113IL_07300.12
114IL_16330.12
115IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
116IL_91132.12
117IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
118IL_23414.12
119IL_40892.12
120IL_90057.12
121IL_98566.12
122IL_73816.12tHS tHH bulge with S-turn
123IL_81441.12
124IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
125IL_31707.12Vitamin B12 aptamer
126IL_09882.12
127IL_28942.12
128IL_82831.22Kink-turn from 16S H23
129IL_00998.12
130IL_74876.12
131IL_83250.1116S h40 3WJ T.th.
132IL_43316.11
133IL_88403.11
134IL_80652.11
135IL_12486.11
136IL_31241.11
137IL_76256.11
138IL_25082.11
139IL_71685.11Sarcin-like with an intercalated basepair
140IL_25181.11
141IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
142IL_60643.11
143IL_03110.11
144IL_41791.11
145IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
146IL_12507.11
147IL_06468.1116S h40 3WJ E.c.
148IL_52958.11
149IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
150IL_97073.11
151IL_54450.11
152IL_71942.11
153IL_53423.11
154IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
155IL_23639.11tWH-tHS-L-cWW
156IL_90880.11
157IL_15205.11
158IL_63952.11
159IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
160IL_86059.11
161IL_80505.11
162IL_61991.11
163IL_47687.11
164IL_22579.11
165IL_67735.11
166IL_76486.11Sarcin-ricin motif with syn G
167IL_37990.11
168IL_17603.11
169IL_85510.11
170IL_92280.11
171IL_39324.11
172IL_82650.11
173IL_06780.11
174IL_55649.11
175IL_52509.11
176IL_37715.11
177IL_55934.11kink-turn-like
178IL_61730.11
179IL_13682.11
180IL_97842.11
181IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
182IL_56513.11
183IL_88367.11
184IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
185IL_40845.11
186IL_57977.11
187IL_76263.11
188IL_25307.11
189IL_26868.11
190IL_78809.11
191IL_06306.11
192IL_37347.11
193IL_46306.11
194IL_21421.11
195IL_40527.11Kink-turn
196IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
197IL_11302.11
198IL_89794.11
199IL_65788.11
200IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
201IL_54576.11
202IL_75415.11Pseudo-knot forming internal loop
203IL_83856.11
204IL_05221.11
205IL_06471.11
206IL_58454.11
207IL_41139.11
208IL_68827.11Reverse Kink-Turn
209IL_98688.11
210IL_66744.11SSU Helix 21 (h21) IL2 E.coli
211IL_53988.11
212IL_20775.11tSH-inserted
213IL_11869.11
214IL_03741.11
215IL_81398.11
216IL_53323.11
217IL_26971.11
218IL_91904.11
219IL_18755.11
220IL_70550.11
221IL_85805.11
222IL_02835.11
223IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
224IL_83920.11
225IL_05462.11
226IL_06808.11Double sheared (tSH-tSH) one bulged base.
227IL_02690.11
228IL_91078.11
229IL_82113.11
230IL_98924.11
231IL_59529.11
232IL_02957.11
233IL_82601.11Tandem cWW water-inserted CU pairs
234IL_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_16377.12
3IL_89231.12LSU H77
4IL_69901.12
5IL_77076.12
6IL_06847.11Group II Intron IL
7IL_77195.11
8IL_77296.11
9IL_17268.11
10IL_91044.11
11IL_47968.11
12IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
13IL_60649.11Kink-turn
14IL_03282.11