Changes in PDB files used for clustering

Release 0.12 has 197 PDB files, release 1.0 has 200 PDB files, 197 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_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
15IL_94430.31516S h32-h33-h34 3WJ
16IL_31555.315Tandem sheared with inserted, unpaired purine.
17IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_27618.21123S H73 ILa : Part of larger Motif
19IL_46648.11123S H91 IL | Single-Base Intercalation Site
20IL_40090.21116S h34 ILa : Part of larger motif
21IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_47444.39SRP Loop E-like motif
24IL_92114.39GAAA loop receptor "platform" motif
25IL_58291.29Recurrent Sub-motif found in junctions
26IL_90459.28cWW AG or UU
27IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
29IL_86357.27LSU Helix 61 IL2
30IL_73000.27cHS-cWS
31IL_25230.26Bacterial 5S rRNA Loop E
32IL_70237.36
33IL_08926.1623S H91 IL
34IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
35IL_97057.26
36IL_54420.16
37IL_72158.26LSU Helix 62 (H62) IL
38IL_53635.26LSU Helix 32 (H32) IL
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_78732.35Double S-turn motif
41IL_01239.15
42IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
43IL_45262.25
44IL_79083.25
45IL_77263.15Kink-turn from U4
46IL_90133.15
47IL_92484.15
48IL_82188.15LSU H68 IL from H.m.
49IL_02359.25
50IL_31066.24SSU Helix 44 (h44) extension
51IL_28572.1416S h18 kink-turn like motif
52IL_38807.24
53IL_22732.14tSH-inserted-tHS
54IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
55IL_21333.14tSH-tHW-bulge
56IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
57IL_98591.24
58IL_40387.44LSU Helix 89 (H89) IL2
59IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
60IL_52173.13
61IL_58586.23
62IL_37053.13Kink-turn from 23S H58
63IL_34363.13Kink-turn from 23S H42
64IL_53774.13Single sheared with bulged bases
65IL_34628.23Kink-turn
66IL_98421.23SSU Helix 12 (h12) IL
67IL_23262.33
68IL_79955.23SSU Helix (23) h23 IL1
69IL_16166.23
70IL_43946.13
71IL_30840.13
72IL_95150.33
73IL_75447.13
74IL_80494.23LSU H58 IL2 H.m.
75IL_36254.13
76IL_82563.13Thi-box riboswitch T-loop
77IL_41397.22LSU Helix 96 (H96) IL2
78IL_23414.12
79IL_40892.12
80IL_89231.12LSU H77
81IL_21495.12
82IL_37406.12
83IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
84IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
85IL_77076.12
86IL_91132.12
87IL_46435.12
88IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
89IL_28942.12
90IL_16377.12
91IL_09882.12
92IL_90057.12
93IL_98566.12
94IL_81441.12
95IL_96446.12
96IL_31707.12Vitamin B12 aptamer
97IL_12211.12
98IL_15840.22Triple Sheared with unpaired, inserted A
99IL_25174.12
100IL_50521.12
101IL_97833.12
102IL_01054.12
103IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
104IL_94744.12Sarcin-ricin motif with extra cWW GA pair
105IL_37197.12
106IL_87548.12
107IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
108IL_52940.12
109IL_65137.12Kink-turn like motif in Group I Intron
110IL_76095.32Motif from Hairpin Ribozyme
111IL_80093.12
112IL_00998.12
113IL_55287.12
114IL_07300.12
115IL_45794.12
116IL_11751.12
117IL_70280.12Double sheared with wobble cWW.
118IL_16330.12
119IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
120IL_68827.11Reverse Kink-Turn
121IL_98688.11
122IL_66744.11SSU Helix 21 (h21) IL2 E.coli
123IL_52958.11
124IL_37715.11
125IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
126IL_78809.11
127IL_83856.11
128IL_37347.11
129IL_46306.11
130IL_58454.11
131IL_41139.11
132IL_03282.11
133IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
134IL_40845.11
135IL_39324.11
136IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
137IL_83920.11
138IL_88403.11
139IL_52509.11
140IL_65788.11
141IL_11869.11
142IL_54576.11
143IL_75415.11Pseudo-knot forming internal loop
144IL_81398.11
145IL_05221.11
146IL_06471.11
147IL_18755.11
148IL_91089.11
149IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
150IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
151IL_57977.11
152IL_06468.1116S h40 3WJ E.c.
153IL_31006.11tSH-tHW-L-bif-cWW
154IL_55649.11
155IL_82113.11
156IL_53323.11
157IL_26971.11
158IL_91904.11
159IL_82601.11Tandem cWW water-inserted CU pairs
160IL_23448.11
161IL_57285.11
162IL_43316.11
163IL_12507.11
164IL_47687.11
165IL_20775.11tSH-inserted
166IL_02690.11
167IL_31241.11
168IL_77014.11
169IL_03741.11
170IL_25082.11
171IL_98924.11
172IL_59529.11
173IL_02957.11
174IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
175IL_60643.11
176IL_85805.11
177IL_80505.11
178IL_61991.11
179IL_89794.11
180IL_05462.11
181IL_06808.11Double sheared (tSH-tSH) one bulged base.
182IL_12486.11
183IL_71942.11
184IL_91078.11
185IL_77195.11
186IL_71685.11Sarcin-like with an intercalated basepair
187IL_25181.11
188IL_90880.11
189IL_15205.11
190IL_91044.11
191IL_27668.11
192IL_83250.1116S h40 3WJ T.th.
193IL_02835.11
194IL_82650.11
195IL_53988.11
196IL_54450.11
197IL_75328.11
198IL_67735.11
199IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
200IL_23639.11tWH-tHS-L-cWW
201IL_17603.11
202IL_85510.11
203IL_06847.11Group II Intron IL
204IL_88865.11
205IL_76263.11
206IL_25307.11
207IL_26868.11
208IL_80652.11
209IL_97073.11
210IL_22579.11
211IL_27243.11
212IL_76486.11Sarcin-ricin motif with syn G
213IL_37990.11
214IL_56513.11
215IL_88367.11
216IL_60649.11Kink-turn
217IL_63952.11
218IL_92280.11
219IL_03110.11
220IL_41791.11
221IL_86059.11
222IL_91379.11
223IL_11302.11
224IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
225IL_55934.11kink-turn-like
226IL_61730.11
227IL_13682.11
228IL_06306.11
229IL_97842.11
230IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
231IL_21421.11
232IL_40527.11Kink-turn
233IL_77296.11

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_62499.53
10IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
11IL_09348.43Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
12IL_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.
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_10005.14
5IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
6IL_91547.13tHS tHH bulge with S-turn
7IL_82831.22Kink-turn from 16S H23
8IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
9IL_58811.12
10IL_33965.12tHS tHH bulge with S-turn
11IL_69901.12
12IL_37150.11tHS tHH bulge with S-turn
13IL_76256.11
14IL_41864.11Part of H71 junction in 23S rRNA from T.th.
15IL_47968.11
16IL_87544.11
17IL_53423.11
18IL_96031.11tHS tHH bulge with S-turn
19IL_97961.11

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_57216.13tHS tHH bulge with S-turn
6IL_05723.13
7IL_48918.13Kink-turn variant
8IL_09520.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
9IL_27892.12
10IL_64648.12tHS tHH bulge with S-turn
11IL_79870.12tHS tHH bulge with S-turn
12IL_42397.12
13IL_06635.12
14IL_11778.11
15IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
16IL_63837.11tHS tHH bulge with S-turn
17IL_03914.11
18IL_03931.1116S h19 IL and 23S H41 IL
19IL_82519.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
20IL_44803.11