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

Loading the Sankey diagram...

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_31555.315Tandem sheared with inserted, unpaired purine.
18IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_94430.31516S h32-h33-h34 3WJ
20IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_40090.21116S h34 ILa : Part of larger motif
22IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_46648.11123S H91 IL | Single-Base Intercalation Site
24IL_27618.21123S H73 ILa : Part of larger Motif
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_86357.27LSU Helix 61 IL2
33IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_73000.27cHS-cWS
35IL_10007.16Single sheared with bulged bases
36IL_54420.16
37IL_08926.1623S H91 IL
38IL_89088.1616S h19 IL and 23S H41 IL
39IL_25230.26Bacterial 5S rRNA Loop E
40IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
41IL_97057.26
42IL_53635.26LSU Helix 32 (H32) IL
43IL_72158.26LSU Helix 62 (H62) IL
44IL_13069.26LSU 3WJ H32-H33-H35A
45IL_70237.36
46IL_24022.26
47IL_79083.25
48IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
49IL_45262.25
50IL_78732.35Double S-turn motif
51IL_02359.25
52IL_90133.15
53IL_77263.15Kink-turn from U4
54IL_01239.15
55IL_92484.15
56IL_82188.15LSU H68 IL from H.m.
57IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
58IL_22732.14tSH-inserted-tHS
59IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60IL_38807.24
61IL_21333.14tSH-tHW-bulge
62IL_31066.24SSU Helix 44 (h44) extension
63IL_39526.34
64IL_28572.1416S h18 kink-turn like motif
65IL_98591.24
66IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
67IL_10005.14
68IL_16252.2323S H91 IL
69IL_98421.23SSU Helix 12 (h12) IL
70IL_80494.23LSU H58 IL2 H.m.
71IL_43946.13
72IL_23262.33
73IL_95150.33
74IL_37053.13Kink-turn from 23S H58
75IL_79955.23SSU Helix (23) h23 IL1
76IL_36254.13
77IL_75447.13
78IL_30840.13
79IL_53774.13Single sheared with bulged bases
80IL_34628.23Kink-turn
81IL_34363.13Kink-turn from 23S H42
82IL_82563.13Thi-box riboswitch T-loop
83IL_16166.23
84IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
85IL_71565.13
86IL_52173.13
87IL_09348.33cWW-L-cWW-cWW
88IL_58586.23
89IL_12211.12
90IL_96446.12
91IL_89231.12LSU H77
92IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
93IL_01054.12
94IL_15840.22Triple Sheared with unpaired, inserted A
95IL_81441.12
96IL_55287.12
97IL_37197.12
98IL_09882.12
99IL_77076.12
100IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
101IL_28942.12
102IL_07300.12
103IL_45794.12
104IL_50521.12
105IL_90057.12
106IL_91132.12
107IL_23414.12
108IL_16330.12
109IL_87548.12
110IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
111IL_52940.12
112IL_65137.12Kink-turn like motif in Group I Intron
113IL_00998.12
114IL_74876.12
115IL_40892.12
116IL_11751.12
117IL_97833.12
118IL_98566.12
119IL_82831.22Kink-turn from 16S H23
120IL_41397.22LSU Helix 96 (H96) IL2
121IL_69901.12
122IL_25174.12
123IL_16377.12
124IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
125IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
126IL_76095.32Motif from Hairpin Ribozyme
127IL_46435.12
128IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
129IL_70280.12Double sheared with wobble cWW.
130IL_94744.12Sarcin-ricin motif with extra cWW GA pair
131IL_21495.12
132IL_37406.12
133IL_31707.12Vitamin B12 aptamer
134IL_80093.12
135IL_86059.11
136IL_80505.11
137IL_61991.11
138IL_47687.11
139IL_31006.11tSH-tHW-L-bif-cWW
140IL_55649.11
141IL_61730.11
142IL_75328.11
143IL_53423.11
144IL_77195.11
145IL_71685.11Sarcin-like with an intercalated basepair
146IL_25181.11
147IL_47968.11
148IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
149IL_60643.11
150IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
151IL_41791.11
152IL_82650.11
153IL_20775.11tSH-inserted
154IL_65788.11
155IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
156IL_78809.11
157IL_67735.11
158IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
159IL_23639.11tWH-tHS-L-cWW
160IL_90880.11
161IL_15205.11
162IL_91044.11
163IL_27668.11
164IL_85805.11
165IL_39324.11
166IL_76263.11
167IL_25307.11
168IL_26868.11
169IL_89794.11
170IL_05462.11
171IL_06808.11Double sheared (tSH-tSH) one bulged base.
172IL_11869.11
173IL_54576.11
174IL_13682.11
175IL_76486.11Sarcin-ricin motif with syn G
176IL_37990.11
177IL_17603.11
178IL_85510.11
179IL_06847.11Group II Intron IL
180IL_83250.1116S h40 3WJ T.th.
181IL_57977.11
182IL_91379.11
183IL_11302.11
184IL_53988.11
185IL_80652.11
186IL_02690.11
187IL_06306.11
188IL_97842.11
189IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
190IL_56513.11
191IL_88367.11
192IL_60649.11Kink-turn
193IL_68827.11Reverse Kink-Turn
194IL_98688.11
195IL_66744.11SSU Helix 21 (h21) IL2 E.coli
196IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
197IL_97073.11
198IL_12486.11
199IL_31241.11
200IL_75415.11Pseudo-knot forming internal loop
201IL_83856.11
202IL_37347.11
203IL_46306.11
204IL_21421.11
205IL_40527.11Kink-turn
206IL_77296.11
207IL_63952.11
208IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
209IL_83920.11
210IL_54450.11
211IL_76256.11
212IL_81398.11
213IL_05221.11
214IL_06471.11
215IL_58454.11
216IL_41139.11
217IL_03282.11
218IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
219IL_88865.11
220IL_88403.11
221IL_52958.11
222IL_52509.11
223IL_22579.11
224IL_77014.11
225IL_03741.11
226IL_82113.11
227IL_53323.11
228IL_26971.11
229IL_91904.11
230IL_18755.11
231IL_91089.11
232IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
233IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
234IL_40845.11
235IL_92280.11
236IL_02835.11
237IL_43316.11
238IL_12507.11
239IL_06468.1116S h40 3WJ E.c.
240IL_37715.11
241IL_55934.11kink-turn-like
242IL_27243.11
243IL_71942.11
244IL_91078.11
245IL_25082.11
246IL_98924.11
247IL_59529.11
248IL_02957.11
249IL_82601.11Tandem cWW water-inserted CU pairs
250IL_23448.11
251IL_57285.11
252IL_03110.11

Updated motif groups

#Motif idInstancesDescription
1IL_47174.5203cWW AG or water inserted cWW Y-Y.
2IL_98556.34
3IL_40387.44LSU Helix 89 (H89) IL2
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_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
6IL_70550.11
7IL_06780.11
8IL_17268.11

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_41864.11Part of H71 junction in 23S rRNA from T.th.
5IL_87544.11
6IL_96031.11tHS tHH bulge with S-turn
7IL_97961.11
8IL_37150.11tHS tHH bulge with S-turn