Changes in PDB files used for clustering

Release 0.9 has 196 PDB files, release 0.10 has 196 PDB files, 194 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_40090.21116S h34 ILa : Part of larger motif
18IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
26IL_73000.27cHS-cWS
27IL_86357.27LSU Helix 61 IL2
28IL_24022.26
29IL_25230.26Bacterial 5S rRNA Loop E
30IL_70237.36
31IL_10007.16Single sheared with bulged bases
32IL_08926.1623S H91 IL
33IL_97057.26
34IL_89088.1616S h19 IL and 23S H41 IL
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_54420.16
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_92484.15
41IL_82188.15LSU H68 IL from H.m.
42IL_78732.35Double S-turn motif
43IL_02359.25
44IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
45IL_45262.25
46IL_77263.15Kink-turn from U4
47IL_01239.15
48IL_90133.15
49IL_79083.25
50IL_39526.34
51IL_28572.1416S h18 kink-turn like motif
52IL_31066.24SSU Helix 44 (h44) extension
53IL_38807.24
54IL_40387.34
55IL_98556.24
56IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
57IL_22732.14tSH-inserted-tHS
58IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
59IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_21333.14tSH-tHW-bulge
61IL_98591.24
62IL_89028.23Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
63IL_62499.33
64IL_58586.23
65IL_80494.23LSU H58 IL2 H.m.
66IL_53774.13Single sheared with bulged bases
67IL_34628.23Kink-turn
68IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
69IL_52173.13
70IL_37053.13Kink-turn from 23S H58
71IL_30840.13
72IL_43946.13
73IL_34363.13Kink-turn from 23S H42
74IL_98421.23SSU Helix 12 (h12) IL
75IL_36254.13
76IL_16166.23
77IL_75447.13
78IL_23262.33
79IL_86826.13tHS tHH bulge with S-turn
80IL_09348.33cWW-L-cWW-cWW
81IL_16252.2323S H91 IL
82IL_95150.33
83IL_79955.23SSU Helix (23) h23 IL1
84IL_71565.13
85IL_82563.13Thi-box riboswitch T-loop
86IL_87548.12
87IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
88IL_52940.12
89IL_65137.12Kink-turn like motif in Group I Intron
90IL_97833.12
91IL_80093.12
92IL_46435.12
93IL_82831.22Kink-turn from 16S H23
94IL_28942.12
95IL_07300.12
96IL_16330.12
97IL_96446.12
98IL_11751.12
99IL_76095.32Motif from Hairpin Ribozyme
100IL_12211.12
101IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
102IL_00998.12
103IL_23414.12
104IL_40892.12
105IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
106IL_34156.32cWW AG or UU
107IL_21495.12
108IL_74876.12
109IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
110IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
111IL_25174.12
112IL_90057.12
113IL_91132.12
114IL_01054.12
115IL_15840.22Triple Sheared with unpaired, inserted A
116IL_37406.12
117IL_41397.22LSU Helix 96 (H96) IL2
118IL_70280.12Double sheared with wobble cWW.
119IL_94744.12Sarcin-ricin motif with extra cWW GA pair
120IL_31707.12Vitamin B12 aptamer
121IL_09882.12
122IL_98566.12
123IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
124IL_37737.12
125IL_93782.12
126IL_73816.12tHS tHH bulge with S-turn
127IL_37197.12
128IL_50521.12
129IL_81441.12
130IL_55287.12
131IL_45794.12
132IL_43316.11
133IL_83920.11
134IL_53988.11
135IL_20775.11tSH-inserted
136IL_11869.11
137IL_54576.11
138IL_13682.11
139IL_97842.11
140IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
141IL_56513.11
142IL_88367.11
143IL_63952.11
144IL_03110.11
145IL_41791.11
146IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
147IL_12507.11
148IL_88403.11
149IL_05462.11
150IL_06808.11Double sheared (tSH-tSH) one bulged base.
151IL_02690.11
152IL_06306.11
153IL_37347.11
154IL_46306.11
155IL_21421.11
156IL_40527.11Kink-turn
157IL_27668.11
158IL_92280.11
159IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
160IL_86059.11
161IL_80505.11
162IL_06468.1116S h40 3WJ E.c.
163IL_80652.11
164IL_12486.11
165IL_31241.11
166IL_75415.11Pseudo-knot forming internal loop
167IL_83856.11
168IL_05221.11
169IL_06471.11
170IL_58454.11
171IL_41139.11
172IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
173IL_40845.11
174IL_39324.11
175IL_82650.11
176IL_61991.11
177IL_47687.11
178IL_52958.11
179IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
180IL_97073.11
181IL_54450.11
182IL_76256.11
183IL_03741.11
184IL_81398.11
185IL_53323.11
186IL_26971.11
187IL_91904.11
188IL_18755.11
189IL_70550.11
190IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
191IL_57977.11
192IL_76263.11
193IL_25307.11
194IL_06780.11
195IL_22579.11
196IL_77014.11
197IL_91078.11
198IL_82113.11
199IL_98924.11
200IL_59529.11
201IL_02957.11
202IL_82601.11Tandem cWW water-inserted CU pairs
203IL_91089.11
204IL_91379.11
205IL_26868.11
206IL_31006.11tSH-tHW-L-bif-cWW
207IL_55649.11
208IL_52509.11
209IL_37715.11
210IL_55934.11kink-turn-like
211IL_27243.11
212IL_71942.11
213IL_25082.11
214IL_71685.11Sarcin-like with an intercalated basepair
215IL_25181.11
216IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
217IL_23448.11
218IL_85805.11
219IL_68827.11Reverse Kink-Turn
220IL_11302.11
221IL_61730.11
222IL_75328.11
223IL_53423.11
224IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
225IL_23639.11tWH-tHS-L-cWW
226IL_90880.11
227IL_15205.11
228IL_60643.11
229IL_83250.1116S h40 3WJ T.th.
230IL_88865.11
231IL_02835.11
232IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
233IL_98688.11
234IL_66744.11SSU Helix 21 (h21) IL2 E.coli
235IL_89794.11
236IL_65788.11
237IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
238IL_78809.11
239IL_67735.11
240IL_76486.11Sarcin-ricin motif with syn G
241IL_37990.11
242IL_17603.11
243IL_85510.11
244IL_57285.11

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_77296.11
7IL_17268.11
8IL_91044.11
9IL_47968.11
10IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
11IL_60649.11Kink-turn
12IL_03282.11
13IL_06847.11Group II Intron IL
14IL_77195.11