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_93424.322tSH-inserted-tHW
11IL_65553.522Kink-turn
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_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_85647.316Sarcin-ricin parent motif with 15 Nts
18IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
19IL_94430.41516S h32-h33-h34 3WJ
20IL_31555.315Tandem sheared with inserted, unpaired purine.
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_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_92114.39GAAA loop receptor "platform" motif
29IL_47444.39SRP Loop E-like motif
30IL_58291.39Recurrent Sub-motif found in junctions
31IL_90459.39cWW AG or UU
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_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36IL_97057.36
37IL_53635.36LSU Helix 32 (H32) IL
38IL_90133.26
39IL_72158.36LSU Helix 62 (H62) IL
40IL_25230.36Bacterial 5S rRNA Loop E
41IL_54420.16
42IL_70237.36
43IL_13069.36LSU 3WJ H32-H33-H35A
44IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
46IL_77263.15Kink-turn from U4
47IL_45262.35
48IL_86357.35LSU Helix 61 IL2
49IL_16207.15Single sheared with bulged bases
50IL_08926.2523S H91 IL
51IL_79083.35
52IL_92484.15
53IL_25300.1516S h19 IL and 23S H41 IL
54IL_82188.15LSU H68 IL from H.m.
55IL_78732.35Double S-turn motif
56IL_02359.35
57IL_39526.44
58IL_28572.1416S h18 kink-turn like motif
59IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_31066.24SSU Helix 44 (h44) extension
61IL_21333.24tSH-tHW-bulge
62IL_42251.14
63IL_38807.34
64IL_01080.14
65IL_16166.3423S H91 IL
66IL_34363.24Kink-turn from 23S H42
67IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
68IL_22732.14tSH-inserted-tHS
69IL_98591.34
70IL_94403.14LSU H77
71IL_08559.14LSU Helix 89 (H89) IL2
72IL_62499.63
73IL_71565.33
74IL_80494.23LSU H58 IL2 H.m.
75IL_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.
76IL_30840.13
77IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
78IL_37053.13Kink-turn from 23S H58
79IL_92267.1323S H73 ILa : Part of larger Motif
80IL_48918.23Kink-turn variant
81IL_80348.1323S H91 IL
82IL_34156.63cWW AG or UU
83IL_10647.13tHS tHH bulge with S-turn
84IL_98421.33SSU Helix 12 (h12) IL
85IL_52173.13
86IL_43946.13
87IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
88IL_56077.13
89IL_34628.23Kink-turn
90IL_95150.33
91IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
92IL_75447.13
93IL_79955.23SSU Helix (23) h23 IL1
94IL_58586.23
95IL_82563.13Thi-box riboswitch T-loop
96IL_05723.13
97IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
98IL_11751.12
99IL_65137.12Kink-turn like motif in Group I Intron
100IL_77076.12
101IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
102IL_55287.12
103IL_19898.12
104IL_90057.12
105IL_12211.12
106IL_21495.12
107IL_09901.12tHS tHH bulge with S-turn
108IL_31707.12Vitamin B12 aptamer
109IL_33925.12
110IL_01054.12
111IL_15840.22Triple Sheared with unpaired, inserted A
112IL_37406.12
113IL_69536.12LSU Helix 96 (H96) IL2
114IL_28942.12
115IL_23414.12
116IL_37197.12
117IL_97833.12
118IL_23262.42
119IL_07300.12
120IL_45794.12
121IL_33964.12
122IL_76095.32Motif from Hairpin Ribozyme
123IL_98566.12
124IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
125IL_70280.12Double sheared with wobble cWW.
126IL_24358.12
127IL_16330.12
128IL_50521.12
129IL_40892.12
130IL_87548.12
131IL_09882.12
132IL_91273.12
133IL_00998.12
134IL_16252.3223S H91 IL
135IL_94744.12Sarcin-ricin motif with extra cWW GA pair
136IL_49550.12tHS tHH bulge with S-turn
137IL_96446.12
138IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
139IL_52940.12
140IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
141IL_80093.12
142IL_46435.12
143IL_09587.12
144IL_27892.12
145IL_88180.12cWW-bulge-cWW
146IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
147IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
148IL_41791.11
149IL_43316.11
150IL_12507.11
151IL_06468.1116S h40 3WJ E.c.
152IL_52958.11
153IL_80652.11
154IL_65788.11
155IL_61730.11
156IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
157IL_25082.11
158IL_98924.11
159IL_59529.11
160IL_02957.11
161IL_28468.11Single sheared with bulged bases
162IL_88367.11
163IL_06847.11Group II Intron IL
164IL_30067.11
165IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
166IL_57977.11
167IL_39324.11
168IL_80505.11
169IL_47687.11
170IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
171IL_97073.11
172IL_03931.1116S h19 IL and 23S H41 IL
173IL_78809.11
174IL_13682.11
175IL_31290.11
176IL_13434.11
177IL_71685.11Sarcin-like with an intercalated basepair
178IL_25181.11
179IL_58454.11
180IL_40527.11Kink-turn
181IL_60649.11Kink-turn
182IL_52610.11
183IL_40845.11
184IL_86059.11
185IL_82650.11
186IL_31006.11tSH-tHW-L-bif-cWW
187IL_21221.11SSU Helix 12 (h12) IL
188IL_54576.11
189IL_67735.11
190IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
191IL_23639.11tWH-tHS-L-cWW
192IL_64589.11
193IL_41139.11
194IL_77296.11
195IL_87394.11
196IL_25307.11
197IL_26868.11
198IL_55649.11
199IL_52509.11
200IL_02690.11
201IL_75415.11Pseudo-knot forming internal loop
202IL_76486.11Sarcin-ricin motif with syn G
203IL_37990.11
204IL_82601.11Tandem cWW water-inserted CU pairs
205IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
206IL_03282.11
207IL_42891.11
208IL_88865.11
209IL_76263.11
210IL_91379.11
211IL_11302.11
212IL_89794.11
213IL_95774.11tHS tHH bulge with S-turn
214IL_12486.11
215IL_06306.11
216IL_97842.11
217IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
218IL_17603.11
219IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
220IL_91089.11
221IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
222IL_47732.11
223IL_85805.11
224IL_92280.11
225IL_68827.11Reverse Kink-Turn
226IL_04550.11tHS tHH bulge with S-turn
227IL_66744.11SSU Helix 21 (h21) IL2 E.coli
228IL_53988.11
229IL_28644.11
230IL_11778.11
231IL_37715.11
232IL_54450.11
233IL_77014.11
234IL_03741.11
235IL_83856.11
236IL_37347.11
237IL_46306.11
238IL_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.
239IL_15205.11
240IL_23448.11
241IL_57285.11
242IL_30354.11
243IL_83250.1116S h40 3WJ T.th.
244IL_02835.11
245IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
246IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
247IL_05462.11
248IL_20775.11tSH-inserted
249IL_71942.11
250IL_91078.11
251IL_81398.11
252IL_05221.11
253IL_06471.11
254IL_91904.11
255IL_56513.11
256IL_60643.11
257IL_46721.11
258IL_63952.11
259IL_03110.11
260IL_83920.11
261IL_06808.11Double sheared (tSH-tSH) one bulged base.
262IL_27243.11
263IL_75328.11
264IL_82113.11
265IL_53323.11
266IL_26971.11
267IL_09491.11
268IL_21421.11
269IL_85510.11
270IL_91044.11
271IL_27668.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription