Changes in PDB files used for clustering

Release 1.2 has 201 PDB files, release 1.3 has 201 PDB files, 201 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_73276.321C-loop
13IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
14IL_55938.318LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.31716S h21 S8 binding site
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
18IL_31555.315Tandem sheared with inserted, unpaired purine.
19IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
20IL_94430.41516S h32-h33-h34 3WJ
21IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_40090.31116S h34 ILa : Part of larger motif
23IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_58291.39Recurrent Sub-motif found in junctions
29IL_90459.39cWW AG or UU
30IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
31IL_92114.39GAAA loop receptor "platform" motif
32IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_73000.27cHS-cWS
35IL_53635.36LSU Helix 32 (H32) IL
36IL_90133.26
37IL_72158.36LSU Helix 62 (H62) IL
38IL_25230.36Bacterial 5S rRNA Loop E
39IL_54420.16
40IL_70237.36
41IL_13069.36LSU 3WJ H32-H33-H35A
42IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
43IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
44IL_97057.36
45IL_08926.2523S H91 IL
46IL_79083.35
47IL_92484.15
48IL_25300.1516S h19 IL and 23S H41 IL
49IL_82188.15LSU H68 IL from H.m.
50IL_78732.35Double S-turn motif
51IL_02359.35
52IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
53IL_77263.15Kink-turn from U4
54IL_45262.35
55IL_86357.35LSU Helix 61 IL2
56IL_16207.15Single sheared with bulged bases
57IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
58IL_22732.14tSH-inserted-tHS
59IL_98591.34
60IL_94403.14LSU H77
61IL_08559.14LSU Helix 89 (H89) IL2
62IL_39526.44
63IL_28572.1416S h18 kink-turn like motif
64IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
65IL_31066.24SSU Helix 44 (h44) extension
66IL_21333.24tSH-tHW-bulge
67IL_42251.14
68IL_38807.34
69IL_01080.14
70IL_16166.3423S H91 IL
71IL_34363.24Kink-turn from 23S H42
72IL_95150.33
73IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
74IL_75447.13
75IL_79955.23SSU Helix (23) h23 IL1
76IL_58586.23
77IL_82563.13Thi-box riboswitch T-loop
78IL_05723.13
79IL_62499.63
80IL_71565.33
81IL_80494.23LSU H58 IL2 H.m.
82IL_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.
83IL_30840.13
84IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
85IL_37053.13Kink-turn from 23S H58
86IL_92267.1323S H73 ILa : Part of larger Motif
87IL_48918.23Kink-turn variant
88IL_80348.1323S H91 IL
89IL_34156.63cWW AG or UU
90IL_10647.13tHS tHH bulge with S-turn
91IL_98421.33SSU Helix 12 (h12) IL
92IL_52173.13
93IL_43946.13
94IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
95IL_56077.13
96IL_34628.23Kink-turn
97IL_76095.32Motif from Hairpin Ribozyme
98IL_98566.12
99IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
100IL_70280.12Double sheared with wobble cWW.
101IL_24358.12
102IL_16330.12
103IL_50521.12
104IL_40892.12
105IL_87548.12
106IL_09882.12
107IL_91273.12
108IL_00998.12
109IL_16252.3223S H91 IL
110IL_94744.12Sarcin-ricin motif with extra cWW GA pair
111IL_49550.12tHS tHH bulge with S-turn
112IL_96446.12
113IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
114IL_52940.12
115IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
116IL_80093.12
117IL_46435.12
118IL_09587.12
119IL_27892.12
120IL_88180.12cWW-bulge-cWW
121IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
122IL_11751.12
123IL_65137.12Kink-turn like motif in Group I Intron
124IL_77076.12
125IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
126IL_55287.12
127IL_19898.12
128IL_90057.12
129IL_12211.12
130IL_21495.12
131IL_09901.12tHS tHH bulge with S-turn
132IL_31707.12Vitamin B12 aptamer
133IL_33925.12
134IL_01054.12
135IL_15840.22Triple Sheared with unpaired, inserted A
136IL_37406.12
137IL_69536.12LSU Helix 96 (H96) IL2
138IL_28942.12
139IL_23414.12
140IL_37197.12
141IL_97833.12
142IL_23262.42
143IL_07300.12
144IL_45794.12
145IL_33964.12
146IL_88865.11
147IL_76263.11
148IL_91379.11
149IL_11302.11
150IL_89794.11
151IL_95774.11tHS tHH bulge with S-turn
152IL_12486.11
153IL_06306.11
154IL_97842.11
155IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
156IL_17603.11
157IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
158IL_91089.11
159IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
160IL_47732.11
161IL_85805.11
162IL_92280.11
163IL_68827.11Reverse Kink-Turn
164IL_04550.11tHS tHH bulge with S-turn
165IL_66744.11SSU Helix 21 (h21) IL2 E.coli
166IL_53988.11
167IL_28644.11
168IL_11778.11
169IL_37715.11
170IL_54450.11
171IL_77014.11
172IL_03741.11
173IL_83856.11
174IL_37347.11
175IL_46306.11
176IL_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.
177IL_15205.11
178IL_23448.11
179IL_57285.11
180IL_30354.11
181IL_83250.1116S h40 3WJ T.th.
182IL_02835.11
183IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
184IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
185IL_05462.11
186IL_20775.11tSH-inserted
187IL_71942.11
188IL_91078.11
189IL_81398.11
190IL_05221.11
191IL_06471.11
192IL_91904.11
193IL_56513.11
194IL_60643.11
195IL_46721.11
196IL_63952.11
197IL_03110.11
198IL_83920.11
199IL_06808.11Double sheared (tSH-tSH) one bulged base.
200IL_27243.11
201IL_75328.11
202IL_82113.11
203IL_53323.11
204IL_26971.11
205IL_09491.11
206IL_21421.11
207IL_85510.11
208IL_91044.11
209IL_27668.11
210IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
211IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
212IL_41791.11
213IL_43316.11
214IL_12507.11
215IL_06468.1116S h40 3WJ E.c.
216IL_52958.11
217IL_80652.11
218IL_65788.11
219IL_61730.11
220IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
221IL_25082.11
222IL_98924.11
223IL_59529.11
224IL_02957.11
225IL_28468.11Single sheared with bulged bases
226IL_88367.11
227IL_06847.11Group II Intron IL
228IL_30067.11
229IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
230IL_57977.11
231IL_39324.11
232IL_80505.11
233IL_47687.11
234IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
235IL_97073.11
236IL_03931.1116S h19 IL and 23S H41 IL
237IL_78809.11
238IL_13682.11
239IL_31290.11
240IL_13434.11
241IL_71685.11Sarcin-like with an intercalated basepair
242IL_25181.11
243IL_58454.11
244IL_40527.11Kink-turn
245IL_60649.11Kink-turn
246IL_52610.11
247IL_40845.11
248IL_86059.11
249IL_82650.11
250IL_31006.11tSH-tHW-L-bif-cWW
251IL_21221.11SSU Helix 12 (h12) IL
252IL_54576.11
253IL_67735.11
254IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
255IL_23639.11tWH-tHS-L-cWW
256IL_64589.11
257IL_41139.11
258IL_77296.11
259IL_87394.11
260IL_25307.11
261IL_26868.11
262IL_55649.11
263IL_52509.11
264IL_02690.11
265IL_75415.11Pseudo-knot forming internal loop
266IL_76486.11Sarcin-ricin motif with syn G
267IL_37990.11
268IL_82601.11Tandem cWW water-inserted CU pairs
269IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
270IL_03282.11
271IL_42891.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription