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: 3G784FAW, 3U4M3UMY.

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_40090.21116S h34 ILa : Part of larger motif
18IL_46648.11123S H91 IL | Single-Base Intercalation Site
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_90459.28cWW AG or UU
24IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
25IL_86357.27LSU Helix 61 IL2
26IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
27IL_73000.27cHS-cWS
28IL_24022.26
29IL_13069.26LSU 3WJ H32-H33-H35A
30IL_10007.16Single sheared with bulged bases
31IL_54420.16
32IL_89088.1616S h19 IL and 23S H41 IL
33IL_72158.26LSU Helix 62 (H62) IL
34IL_08926.1623S H91 IL
35IL_25230.26Bacterial 5S rRNA Loop E
36IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
37IL_70237.36
38IL_53635.26LSU Helix 32 (H32) IL
39IL_97057.26
40IL_45262.25
41IL_77263.15Kink-turn from U4
42IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
43IL_78732.35Double S-turn motif
44IL_79083.25
45IL_01239.15
46IL_82188.15LSU H68 IL from H.m.
47IL_90133.15
48IL_02359.25
49IL_92484.15
50IL_21333.14tSH-tHW-bulge
51IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
52IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
53IL_39526.34
54IL_22732.14tSH-inserted-tHS
55IL_28572.1416S h18 kink-turn like motif
56IL_40387.34
57IL_98556.24
58IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
59IL_31066.24SSU Helix 44 (h44) extension
60IL_38807.24
61IL_98591.24
62IL_09348.33cWW-L-cWW-cWW
63IL_37053.13Kink-turn from 23S H58
64IL_53774.13Single sheared with bulged bases
65IL_52173.13
66IL_58586.23
67IL_89028.23Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
68IL_71565.13
69IL_75447.13
70IL_86826.13tHS tHH bulge with S-turn
71IL_98421.23SSU Helix 12 (h12) IL
72IL_23262.33
73IL_34363.13Kink-turn from 23S H42
74IL_43946.13
75IL_79955.23SSU Helix (23) h23 IL1
76IL_95150.33
77IL_16166.23
78IL_30840.13
79IL_34628.23Kink-turn
80IL_82563.13Thi-box riboswitch T-loop
81IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
82IL_16252.2323S H91 IL
83IL_36254.13
84IL_62499.33
85IL_80494.23LSU H58 IL2 H.m.
86IL_16330.12
87IL_50521.12
88IL_73816.12tHS tHH bulge with S-turn
89IL_09882.12
90IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
91IL_31707.12Vitamin B12 aptamer
92IL_37197.12
93IL_41397.22LSU Helix 96 (H96) IL2
94IL_45794.12
95IL_74876.12
96IL_82831.22Kink-turn from 16S H23
97IL_21495.12
98IL_65137.12Kink-turn like motif in Group I Intron
99IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
100IL_91132.12
101IL_93782.12
102IL_97833.12
103IL_00998.12
104IL_37406.12
105IL_46435.12
106IL_52940.12
107IL_81441.12
108IL_01054.12
109IL_11751.12
110IL_25174.12
111IL_34156.32cWW AG or UU
112IL_90057.12
113IL_94744.12Sarcin-ricin motif with extra cWW GA pair
114IL_07300.12
115IL_15840.22Triple Sheared with unpaired, inserted A
116IL_28942.12
117IL_37737.12
118IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
119IL_76095.32Motif from Hairpin Ribozyme
120IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
121IL_12211.12
122IL_23414.12
123IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
124IL_80093.12
125IL_87548.12
126IL_98566.12
127IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
128IL_40892.12
129IL_55287.12
130IL_70280.12Double sheared with wobble cWW.
131IL_12507.11
132IL_25307.11
133IL_31241.11
134IL_41139.11
135IL_55649.11
136IL_58454.11
137IL_70550.11
138IL_80505.11
139IL_82650.11
140IL_85805.11
141IL_88403.11
142IL_91078.11
143IL_97073.11
144IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
145IL_02835.11
146IL_06468.1116S h40 3WJ E.c.
147IL_21421.11
148IL_26868.11
149IL_39324.11
150IL_53988.11
151IL_55934.11kink-turn-like
152IL_63952.11
153IL_80652.11
154IL_86059.11
155IL_91089.11
156IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
157IL_98688.11
158IL_02957.11
159IL_06471.11
160IL_13682.11
161IL_17603.11
162IL_26971.11
163IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
164IL_37347.11
165IL_46306.11
166IL_52509.11
167IL_59529.11
168IL_75415.11Pseudo-knot forming internal loop
169IL_81398.11
170IL_83250.1116S h40 3WJ T.th.
171IL_98924.11
172IL_03110.11
173IL_06780.11
174IL_11302.11
175IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
176IL_22579.11
177IL_25082.11
178IL_41791.11
179IL_54450.11
180IL_60643.11
181IL_65788.11
182IL_71685.11Sarcin-like with an intercalated basepair
183IL_78809.11
184IL_89794.11
185IL_91904.11
186IL_97842.11
187IL_03741.11
188IL_06808.11Double sheared (tSH-tSH) one bulged base.
189IL_15205.11
190IL_18755.11
191IL_37715.11
192IL_43316.11
193IL_52958.11
194IL_54576.11
195IL_56513.11
196IL_61730.11
197IL_66744.11SSU Helix 21 (h21) IL2 E.coli
198IL_71942.11
199IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
200IL_82113.11
201IL_83856.11
202IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
203IL_05221.11
204IL_11869.11
205IL_20775.11tSH-inserted
206IL_25181.11
207IL_40527.11Kink-turn
208IL_47687.11
209IL_53323.11
210IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
211IL_61991.11
212IL_67735.11
213IL_83920.11
214IL_92280.11
215IL_05462.11
216IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
217IL_37990.11
218IL_40845.11
219IL_53423.11
220IL_57977.11
221IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
222IL_76256.11
223IL_85510.11
224IL_02690.11
225IL_06306.11
226IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
227IL_12486.11
228IL_23639.11tWH-tHS-L-cWW
229IL_76486.11Sarcin-ricin motif with syn G
230IL_82601.11Tandem cWW water-inserted CU pairs
231IL_88367.11
232IL_90880.11

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_77076.12
3IL_16377.12
4IL_89231.12LSU H77
5IL_69901.12
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
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