Changes in PDB files used for clustering

Release 0.12 has 196 PDB files, release 1.0 has 199 PDB files, 196 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.0: 3W3S, 4ANG, 4B5R.

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 0.12 has 266 motif groups, release 1.0 has 267 motif groups, 233 of them are identical.

14 motif groups were updated, 19 groups are present only in release 0.12, 20 groups are only in release 1.0.

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_47174.5203cWW AG or water inserted cWW Y-Y.
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_13959.224Double Sheared (tSH-tHS)
8IL_93424.222tSH-inserted-tHW
9IL_65553.422Kink-turn
10IL_73276.120C-loop
11IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
12IL_92027.21716S h21 S8 binding site
13IL_85647.216Sarcin-ricin parent motif with 15 Nts
14IL_31555.315Tandem sheared with inserted, unpaired purine.
15IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_94430.31516S h32-h33-h34 3WJ
17IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_46648.11123S H91 IL | Single-Base Intercalation Site
19IL_27618.21123S H73 ILa : Part of larger Motif
20IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21IL_40090.21116S h34 ILa : Part of larger motif
22IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_47444.39SRP Loop E-like motif
24IL_58291.29Recurrent Sub-motif found in junctions
25IL_92114.39GAAA loop receptor "platform" motif
26IL_90459.28cWW AG or UU
27IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28IL_86357.27LSU Helix 61 IL2
29IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
30IL_73000.27cHS-cWS
31IL_08926.1623S H91 IL
32IL_97057.26
33IL_13069.26LSU 3WJ H32-H33-H35A
34IL_70237.36
35IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36IL_53635.26LSU Helix 32 (H32) IL
37IL_25230.26Bacterial 5S rRNA Loop E
38IL_72158.26LSU Helix 62 (H62) IL
39IL_54420.16
40IL_01239.15
41IL_77263.15Kink-turn from U4
42IL_92484.15
43IL_02359.25
44IL_78732.35Double S-turn motif
45IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
46IL_45262.25
47IL_90133.15
48IL_79083.25
49IL_82188.15LSU H68 IL from H.m.
50IL_21333.14tSH-tHW-bulge
51IL_40387.44LSU Helix 89 (H89) IL2
52IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
53IL_28572.1416S h18 kink-turn like motif
54IL_22732.14tSH-inserted-tHS
55IL_38807.24
56IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
57IL_31066.24SSU Helix 44 (h44) extension
58IL_98591.24
59IL_80494.23LSU H58 IL2 H.m.
60IL_43946.13
61IL_75447.13
62IL_34363.13Kink-turn from 23S H42
63IL_34628.23Kink-turn
64IL_23262.33
65IL_30840.13
66IL_36254.13
67IL_53774.13Single sheared with bulged bases
68IL_58586.23
69IL_98421.23SSU Helix 12 (h12) IL
70IL_16166.23
71IL_37053.13Kink-turn from 23S H58
72IL_79955.23SSU Helix (23) h23 IL1
73IL_95150.33
74IL_52173.13
75IL_82563.13Thi-box riboswitch T-loop
76IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
77IL_16377.12
78IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
79IL_31707.12Vitamin B12 aptamer
80IL_37406.12
81IL_52940.12
82IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
83IL_89231.12LSU H77
84IL_09882.12
85IL_21495.12
86IL_70280.12Double sheared with wobble cWW.
87IL_91132.12
88IL_25174.12
89IL_40892.12
90IL_55287.12
91IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
92IL_90057.12
93IL_97833.12
94IL_11751.12
95IL_28942.12
96IL_65137.12Kink-turn like motif in Group I Intron
97IL_76095.32Motif from Hairpin Ribozyme
98IL_81441.12
99IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
100IL_94744.12Sarcin-ricin motif with extra cWW GA pair
101IL_15840.22Triple Sheared with unpaired, inserted A
102IL_41397.22LSU Helix 96 (H96) IL2
103IL_45794.12
104IL_87548.12
105IL_00998.12
106IL_12211.12
107IL_23414.12
108IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
109IL_50521.12
110IL_77076.12
111IL_98566.12
112IL_01054.12
113IL_07300.12
114IL_16330.12
115IL_37197.12
116IL_46435.12
117IL_80093.12
118IL_05221.11
119IL_12507.11
120IL_26868.11
121IL_37347.11
122IL_43316.11
123IL_52509.11
124IL_54450.11
125IL_56513.11
126IL_60649.11Kink-turn
127IL_67735.11
128IL_82601.11Tandem cWW water-inserted CU pairs
129IL_85805.11
130IL_88403.11
131IL_91078.11
132IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
133IL_05462.11
134IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
135IL_21421.11
136IL_26971.11
137IL_40527.11Kink-turn
138IL_54576.11
139IL_61730.11
140IL_75415.11Pseudo-knot forming internal loop
141IL_77296.11
142IL_80505.11
143IL_82650.11
144IL_86059.11
145IL_91089.11
146IL_97073.11
147IL_98688.11
148IL_02690.11
149IL_06306.11
150IL_13682.11
151IL_17603.11
152IL_25082.11
153IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
154IL_37715.11
155IL_40845.11
156IL_52958.11
157IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
158IL_57977.11
159IL_61991.11
160IL_80652.11
161IL_83250.1116S h40 3WJ T.th.
162IL_89794.11
163IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
164IL_98924.11
165IL_02835.11
166IL_06468.1116S h40 3WJ E.c.
167IL_11302.11
168IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
169IL_22579.11
170IL_37990.11
171IL_47687.11
172IL_53323.11
173IL_63952.11
174IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
175IL_81398.11
176IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
177IL_91904.11
178IL_02957.11
179IL_06471.11
180IL_15205.11
181IL_18755.11
182IL_25181.11
183IL_41139.11
184IL_55649.11
185IL_58454.11
186IL_71685.11Sarcin-like with an intercalated basepair
187IL_78809.11
188IL_83856.11
189IL_97842.11
190IL_03110.11
191IL_06808.11Double sheared (tSH-tSH) one bulged base.
192IL_11869.11
193IL_20775.11tSH-inserted
194IL_55934.11kink-turn-like
195IL_71942.11
196IL_76486.11Sarcin-ricin motif with syn G
197IL_82113.11
198IL_83920.11
199IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
200IL_03282.11
201IL_06847.11Group II Intron IL
202IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
203IL_39324.11
204IL_46306.11
205IL_53988.11
206IL_59529.11
207IL_65788.11
208IL_85510.11
209IL_90880.11
210IL_92280.11
211IL_03741.11
212IL_12486.11
213IL_23639.11tWH-tHS-L-cWW
214IL_25307.11
215IL_31241.11
216IL_41791.11
217IL_60643.11
218IL_66744.11SSU Helix 21 (h21) IL2 E.coli
219IL_77195.11
220IL_88367.11
221IL_91044.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.52391-3 bulged nucleotides, same chain
2IL_06390.226cWH basepair with syn base
3IL_06429.315cWW-bulge-cWW
4IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
5IL_10007.27Single sheared with bulged bases
6IL_98556.44
7IL_39526.44
8IL_71565.24
9IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
10IL_09348.43Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
11IL_89028.43Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
12IL_62499.53
13IL_16252.3223S H91 IL
14IL_34156.52cWW AG or UU

Removed motif groups

#Motif idInstancesDescription
1IL_32390.22116S h19 IL and 23S H41 IL
2IL_89088.1616S h19 IL and 23S H41 IL
3IL_24022.26
4IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
5IL_10005.14
6IL_91547.13tHS tHH bulge with S-turn
7IL_33965.12tHS tHH bulge with S-turn
8IL_69901.12
9IL_82831.22Kink-turn from 16S H23
10IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
11IL_58811.12
12IL_97961.11
13IL_37150.11tHS tHH bulge with S-turn
14IL_76256.11
15IL_41864.11Part of H71 junction in 23S rRNA from T.th.
16IL_47968.11
17IL_87544.11
18IL_53423.11
19IL_96031.11tHS tHH bulge with S-turn

Added motif groups

#Motif idInstancesDescription
1IL_91487.12116S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_38960.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
3IL_25300.1516S h19 IL and 23S H41 IL
4IL_87218.1423S H91 IL
5IL_05723.13
6IL_48918.13Kink-turn variant
7IL_57216.13tHS tHH bulge with S-turn
8IL_06635.12
9IL_09520.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
10IL_27892.12
11IL_64648.12tHS tHH bulge with S-turn
12IL_79870.12tHS tHH bulge with S-turn
13IL_42397.12
14IL_44803.11
15IL_11778.11
16IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
17IL_63837.11tHS tHH bulge with S-turn
18IL_03914.11
19IL_03931.1116S h19 IL and 23S H41 IL
20IL_82519.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena