Changes in PDB files used for clustering

Release 1.2 has 200 PDB files, release 1.3 has 200 PDB files, 200 of them are identical.

No equivalence class representatives have been replaced.

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 1.2 has 271 motif groups, release 1.3 has 271 motif groups, 271 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.2, 0 groups are only in release 1.3.

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_97217.62391-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.6201cWW AG or water inserted cWW Y-Y.
3IL_39199.354Hoogsteen-edge Platform, Single bulged base
4IL_41766.349Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.343Sugar-edge, 1-base platform, consensus tHS
7IL_87904.431Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.326cWH basepair with syn base
9IL_13959.324Double Sheared (tSH-tHS)
10IL_65553.522Kink-turn
11IL_93424.322tSH-inserted-tHW
12IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
13IL_73276.321C-loop
14IL_55938.318LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_85647.316Sarcin-ricin parent motif with 15 Nts
18IL_94430.41516S h32-h33-h34 3WJ
19IL_31555.315Tandem sheared with inserted, unpaired purine.
20IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
21IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_40090.31116S h34 ILa : Part of larger motif
24IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
25IL_46648.21123S H91 IL | Single-Base Intercalation Site
26IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_47444.39SRP Loop E-like motif
28IL_90459.39cWW AG or UU
29IL_92114.39GAAA loop receptor "platform" motif
30IL_58291.39Recurrent Sub-motif found in junctions
31IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_73000.27cHS-cWS
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_54420.16
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_72158.36LSU Helix 62 (H62) IL
38IL_70237.36
39IL_25230.36Bacterial 5S rRNA Loop E
40IL_53635.36LSU Helix 32 (H32) IL
41IL_97057.36
42IL_13069.36LSU 3WJ H32-H33-H35A
43IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
44IL_90133.26
45IL_08926.2523S H91 IL
46IL_25300.1516S h19 IL and 23S H41 IL
47IL_45262.35
48IL_79083.35
49IL_82188.15LSU H68 IL from H.m.
50IL_02359.35
51IL_77263.15Kink-turn from U4
52IL_92484.15
53IL_78732.35Double S-turn motif
54IL_86357.35LSU Helix 61 IL2
55IL_16207.15Single sheared with bulged bases
56IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
57IL_39526.44
58IL_01080.14
59IL_21333.24tSH-tHW-bulge
60IL_42251.14
61IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
62IL_22732.14tSH-inserted-tHS
63IL_31066.24SSU Helix 44 (h44) extension
64IL_34363.24Kink-turn from 23S H42
65IL_16166.3423S H91 IL
66IL_28572.1416S h18 kink-turn like motif
67IL_38807.34
68IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
69IL_98591.34
70IL_08559.14LSU Helix 89 (H89) IL2
71IL_94403.14LSU H77
72IL_10647.13tHS tHH bulge with S-turn
73IL_37053.13Kink-turn from 23S H58
74IL_52173.13
75IL_71565.33
76IL_75447.13
77IL_92267.1323S H73 ILa : Part of larger Motif
78IL_79955.23SSU Helix (23) h23 IL1
79IL_82563.13Thi-box riboswitch T-loop
80IL_95150.33
81IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
82IL_30840.13
83IL_34156.63cWW AG or UU
84IL_48918.23Kink-turn variant
85IL_62499.63
86IL_80348.1323S H91 IL
87IL_89028.53Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
88IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
89IL_98421.33SSU Helix 12 (h12) IL
90IL_80494.23LSU H58 IL2 H.m.
91IL_34628.23Kink-turn
92IL_43946.13
93IL_58586.23
94IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
95IL_05723.13
96IL_56077.13
97IL_00998.12
98IL_16252.3223S H91 IL
99IL_28942.12
100IL_31707.12Vitamin B12 aptamer
101IL_87548.12
102IL_01054.12
103IL_16330.12
104IL_24358.12
105IL_37197.12
106IL_76095.32Motif from Hairpin Ribozyme
107IL_94744.12Sarcin-ricin motif with extra cWW GA pair
108IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
109IL_11751.12
110IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
111IL_33925.12
112IL_45794.12
113IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
114IL_88180.12cWW-bulge-cWW
115IL_97833.12
116IL_33964.12
117IL_37406.12
118IL_52940.12
119IL_77076.12
120IL_80093.12
121IL_12211.12
122IL_21495.12
123IL_27892.12
124IL_46435.12
125IL_55287.12
126IL_69536.12LSU Helix 96 (H96) IL2
127IL_91273.12
128IL_09587.12
129IL_15840.22Triple Sheared with unpaired, inserted A
130IL_19898.12
131IL_98566.12
132IL_07300.12
133IL_09882.12
134IL_23262.42
135IL_40892.12
136IL_49550.12tHS tHH bulge with S-turn
137IL_70280.12Double sheared with wobble cWW.
138IL_90057.12
139IL_09901.12tHS tHH bulge with S-turn
140IL_23414.12
141IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
142IL_50521.12
143IL_65137.12Kink-turn like motif in Group I Intron
144IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
145IL_03110.11
146IL_06306.11
147IL_13434.11
148IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
149IL_23639.11tWH-tHS-L-cWW
150IL_39324.11
151IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
152IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
153IL_78809.11
154IL_81398.11
155IL_83856.11
156IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
157IL_98924.11
158IL_03282.11
159IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
160IL_11302.11
161IL_13682.11
162IL_25307.11
163IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
164IL_47687.11
165IL_52509.11
166IL_54450.11
167IL_56513.11
168IL_60643.11
169IL_65788.11
170IL_71685.11Sarcin-like with an intercalated basepair
171IL_82113.11
172IL_83920.11
173IL_91044.11
174IL_03741.11
175IL_06468.1116S h40 3WJ E.c.
176IL_26868.11
177IL_30067.11
178IL_37347.11
179IL_41791.11
180IL_47732.11
181IL_52610.11
182IL_54576.11
183IL_60649.11Kink-turn
184IL_66744.11SSU Helix 21 (h21) IL2 E.coli
185IL_71942.11
186IL_76486.11Sarcin-ricin motif with syn G
187IL_85510.11
188IL_91078.11
189IL_92280.11
190IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
191IL_03931.1116S h19 IL and 23S H41 IL
192IL_06471.11
193IL_09491.11
194IL_11778.11
195IL_15205.11
196IL_17603.11
197IL_21421.11
198IL_26971.11
199IL_30354.11
200IL_46306.11
201IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
202IL_57977.11
203IL_61730.11
204IL_67735.11
205IL_88367.11
206IL_91089.11
207IL_97842.11
208IL_02690.11
209IL_04550.11tHS tHH bulge with S-turn
210IL_06808.11Double sheared (tSH-tSH) one bulged base.
211IL_15674.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
212IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
213IL_25082.11
214IL_37715.11
215IL_40527.11Kink-turn
216IL_52958.11
217IL_82601.11Tandem cWW water-inserted CU pairs
218IL_85805.11
219IL_05221.11
220IL_06847.11Group II Intron IL
221IL_12486.11
222IL_25181.11
223IL_28468.11Single sheared with bulged bases
224IL_37990.11
225IL_40845.11
226IL_43316.11
227IL_53323.11
228IL_55649.11
229IL_58454.11
230IL_63952.11
231IL_77296.11
232IL_82650.11
233IL_86059.11
234IL_89794.11
235IL_91904.11
236IL_95774.11tHS tHH bulge with S-turn
237IL_02835.11
238IL_05462.11
239IL_12507.11
240IL_20775.11tSH-inserted
241IL_31290.11
242IL_46721.11
243IL_64589.11
244IL_80505.11
245IL_83250.1116S h40 3WJ T.th.
246IL_02957.11
247IL_21221.11SSU Helix 12 (h12) IL
248IL_28644.11
249IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
250IL_41139.11
251IL_53988.11
252IL_59529.11
253IL_75415.11Pseudo-knot forming internal loop
254IL_80652.11
255IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
256IL_97073.11
257IL_98655.11Part of H71 Junction in 26S rRNA from Yeast

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription