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_93424.322tSH-inserted-tHW
11IL_65553.522Kink-turn
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_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_46648.21123S H91 IL | Single-Base Intercalation Site
23IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_40090.31116S h34 ILa : Part of larger motif
25IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
26IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_47444.39SRP Loop E-like motif
28IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
29IL_92114.39GAAA loop receptor "platform" motif
30IL_58291.39Recurrent Sub-motif found in junctions
31IL_90459.39cWW AG or UU
32IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_73000.27cHS-cWS
34IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
35IL_13069.36LSU 3WJ H32-H33-H35A
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_54420.16
38IL_70237.36
39IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
40IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
41IL_97057.36
42IL_53635.36LSU Helix 32 (H32) IL
43IL_90133.26
44IL_72158.36LSU Helix 62 (H62) IL
45IL_92484.15
46IL_78732.35Double S-turn motif
47IL_82188.15LSU H68 IL from H.m.
48IL_25300.1516S h19 IL and 23S H41 IL
49IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
50IL_77263.15Kink-turn from U4
51IL_45262.35
52IL_79083.35
53IL_86357.35LSU Helix 61 IL2
54IL_16207.15Single sheared with bulged bases
55IL_08926.2523S H91 IL
56IL_02359.35
57IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
58IL_22732.14tSH-inserted-tHS
59IL_98591.34
60IL_39526.44
61IL_94403.14LSU H77
62IL_28572.1416S h18 kink-turn like motif
63IL_42251.14
64IL_38807.34
65IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
66IL_31066.24SSU Helix 44 (h44) extension
67IL_21333.24tSH-tHW-bulge
68IL_34363.24Kink-turn from 23S H42
69IL_01080.14
70IL_16166.3423S H91 IL
71IL_08559.14LSU Helix 89 (H89) IL2
72IL_58586.23
73IL_30840.13
74IL_79955.23SSU Helix (23) h23 IL1
75IL_05723.13
76IL_80494.23LSU H58 IL2 H.m.
77IL_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.
78IL_34628.23Kink-turn
79IL_62499.63
80IL_71565.33
81IL_37053.13Kink-turn from 23S H58
82IL_92267.1323S H73 ILa : Part of larger Motif
83IL_56077.13
84IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
85IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
86IL_34156.63cWW AG or UU
87IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
88IL_80348.1323S H91 IL
89IL_43946.13
90IL_98421.33SSU Helix 12 (h12) IL
91IL_52173.13
92IL_75447.13
93IL_48918.23Kink-turn variant
94IL_95150.33
95IL_82563.13Thi-box riboswitch T-loop
96IL_10647.13tHS tHH bulge with S-turn
97IL_50521.12
98IL_09587.12
99IL_07300.12
100IL_45794.12
101IL_33964.12
102IL_87548.12
103IL_09882.12
104IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
105IL_80093.12
106IL_46435.12
107IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
108IL_09901.12tHS tHH bulge with S-turn
109IL_24358.12
110IL_16330.12
111IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
112IL_52940.12
113IL_21495.12
114IL_37406.12
115IL_69536.12LSU Helix 96 (H96) IL2
116IL_28942.12
117IL_40892.12
118IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
119IL_11751.12
120IL_65137.12Kink-turn like motif in Group I Intron
121IL_77076.12
122IL_12211.12
123IL_01054.12
124IL_15840.22Triple Sheared with unpaired, inserted A
125IL_23262.42
126IL_49550.12tHS tHH bulge with S-turn
127IL_19898.12
128IL_90057.12
129IL_33925.12
130IL_70280.12Double sheared with wobble cWW.
131IL_88180.12cWW-bulge-cWW
132IL_31707.12Vitamin B12 aptamer
133IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
134IL_55287.12
135IL_97833.12
136IL_98566.12
137IL_00998.12
138IL_16252.3223S H91 IL
139IL_94744.12Sarcin-ricin motif with extra cWW GA pair
140IL_76095.32Motif from Hairpin Ribozyme
141IL_91273.12
142IL_27892.12
143IL_23414.12
144IL_37197.12
145IL_85805.11
146IL_92280.11
147IL_02835.11
148IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
149IL_83920.11
150IL_52958.11
151IL_80652.11
152IL_65788.11
153IL_78809.11
154IL_75415.11Pseudo-knot forming internal loop
155IL_76486.11Sarcin-ricin motif with syn G
156IL_37990.11
157IL_82601.11Tandem cWW water-inserted CU pairs
158IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
159IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
160IL_83250.1116S h40 3WJ T.th.
161IL_03110.11
162IL_06468.1116S h40 3WJ E.c.
163IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
164IL_97073.11
165IL_03931.1116S h19 IL and 23S H41 IL
166IL_54576.11
167IL_06306.11
168IL_97842.11
169IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
170IL_17603.11
171IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
172IL_91089.11
173IL_30067.11
174IL_63952.11
175IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
176IL_41791.11
177IL_43316.11
178IL_12507.11
179IL_47687.11
180IL_21221.11SSU Helix 12 (h12) IL
181IL_03741.11
182IL_83856.11
183IL_37347.11
184IL_46306.11
185IL_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.
186IL_15205.11
187IL_60643.11
188IL_52610.11
189IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
190IL_57977.11
191IL_39324.11
192IL_80505.11
193IL_55649.11
194IL_52509.11
195IL_02690.11
196IL_91078.11
197IL_81398.11
198IL_05221.11
199IL_06471.11
200IL_91904.11
201IL_56513.11
202IL_91044.11
203IL_87394.11
204IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
205IL_86059.11
206IL_82650.11
207IL_26868.11
208IL_89794.11
209IL_95774.11tHS tHH bulge with S-turn
210IL_12486.11
211IL_71942.11
212IL_82113.11
213IL_53323.11
214IL_26971.11
215IL_09491.11
216IL_21421.11
217IL_85510.11
218IL_06847.11Group II Intron IL
219IL_42891.11
220IL_40845.11
221IL_25307.11
222IL_11302.11
223IL_53988.11
224IL_28644.11
225IL_11778.11
226IL_37715.11
227IL_54450.11
228IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
229IL_25082.11
230IL_98924.11
231IL_59529.11
232IL_02957.11
233IL_28468.11Single sheared with bulged bases
234IL_88367.11
235IL_60649.11Kink-turn
236IL_47732.11
237IL_76263.11
238IL_04550.11tHS tHH bulge with S-turn
239IL_66744.11SSU Helix 21 (h21) IL2 E.coli
240IL_05462.11
241IL_20775.11tSH-inserted
242IL_13682.11
243IL_31290.11
244IL_13434.11
245IL_71685.11Sarcin-like with an intercalated basepair
246IL_25181.11
247IL_58454.11
248IL_40527.11Kink-turn
249IL_77296.11
250IL_30354.11
251IL_68827.11Reverse Kink-Turn
252IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
253IL_06808.11Double sheared (tSH-tSH) one bulged base.
254IL_61730.11
255IL_67735.11
256IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
257IL_23639.11tWH-tHS-L-cWW
258IL_64589.11
259IL_41139.11
260IL_03282.11
261IL_46721.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription