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_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_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_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_92114.39GAAA loop receptor "platform" motif
29IL_58291.39Recurrent Sub-motif found in junctions
30IL_90459.39cWW AG or UU
31IL_47444.39SRP Loop E-like motif
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_13069.36LSU 3WJ H32-H33-H35A
41IL_25230.36Bacterial 5S rRNA Loop E
42IL_54420.16
43IL_70237.36
44IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45IL_77263.15Kink-turn from U4
46IL_45262.35
47IL_86357.35LSU Helix 61 IL2
48IL_16207.15Single sheared with bulged bases
49IL_02359.35
50IL_08926.2523S H91 IL
51IL_78732.35Double S-turn motif
52IL_92484.15
53IL_82188.15LSU H68 IL from H.m.
54IL_25300.1516S h19 IL and 23S H41 IL
55IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
56IL_79083.35
57IL_28572.1416S h18 kink-turn like motif
58IL_42251.14
59IL_38807.34
60IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
61IL_31066.24SSU Helix 44 (h44) extension
62IL_21333.24tSH-tHW-bulge
63IL_34363.24Kink-turn from 23S H42
64IL_08559.14LSU Helix 89 (H89) IL2
65IL_01080.14
66IL_16166.3423S H91 IL
67IL_39526.44
68IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
69IL_22732.14tSH-inserted-tHS
70IL_98591.34
71IL_94403.14LSU H77
72IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
73IL_34156.63cWW AG or UU
74IL_75447.13
75IL_48918.23Kink-turn variant
76IL_80348.1323S H91 IL
77IL_43946.13
78IL_82563.13Thi-box riboswitch T-loop
79IL_10647.13tHS tHH bulge with S-turn
80IL_98421.33SSU Helix 12 (h12) IL
81IL_52173.13
82IL_30840.13
83IL_95150.33
84IL_58586.23
85IL_34628.23Kink-turn
86IL_79955.23SSU Helix (23) h23 IL1
87IL_05723.13
88IL_56077.13
89IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
90IL_80494.23LSU H58 IL2 H.m.
91IL_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.
92IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
93IL_62499.63
94IL_71565.33
95IL_37053.13Kink-turn from 23S H58
96IL_92267.1323S H73 ILa : Part of larger Motif
97IL_19898.12
98IL_90057.12
99IL_33925.12
100IL_00998.12
101IL_16252.3223S H91 IL
102IL_94744.12Sarcin-ricin motif with extra cWW GA pair
103IL_31707.12Vitamin B12 aptamer
104IL_91273.12
105IL_27892.12
106IL_23414.12
107IL_37197.12
108IL_97833.12
109IL_98566.12
110IL_09587.12
111IL_07300.12
112IL_45794.12
113IL_33964.12
114IL_76095.32Motif from Hairpin Ribozyme
115IL_46435.12
116IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
117IL_09901.12tHS tHH bulge with S-turn
118IL_24358.12
119IL_16330.12
120IL_50521.12
121IL_21495.12
122IL_37406.12
123IL_69536.12LSU Helix 96 (H96) IL2
124IL_28942.12
125IL_40892.12
126IL_87548.12
127IL_09882.12
128IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
129IL_80093.12
130IL_01054.12
131IL_15840.22Triple Sheared with unpaired, inserted A
132IL_23262.42
133IL_49550.12tHS tHH bulge with S-turn
134IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
135IL_52940.12
136IL_70280.12Double sheared with wobble cWW.
137IL_88180.12cWW-bulge-cWW
138IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
139IL_11751.12
140IL_65137.12Kink-turn like motif in Group I Intron
141IL_77076.12
142IL_12211.12
143IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
144IL_55287.12
145IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
146IL_86059.11
147IL_04550.11tHS tHH bulge with S-turn
148IL_66744.11SSU Helix 21 (h21) IL2 E.coli
149IL_05462.11
150IL_20775.11tSH-inserted
151IL_13682.11
152IL_31290.11
153IL_13434.11
154IL_71685.11Sarcin-like with an intercalated basepair
155IL_25181.11
156IL_58454.11
157IL_40527.11Kink-turn
158IL_77296.11
159IL_40845.11
160IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
161IL_06808.11Double sheared (tSH-tSH) one bulged base.
162IL_61730.11
163IL_67735.11
164IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
165IL_23639.11tWH-tHS-L-cWW
166IL_64589.11
167IL_41139.11
168IL_03282.11
169IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
170IL_83920.11
171IL_52958.11
172IL_80652.11
173IL_65788.11
174IL_78809.11
175IL_75415.11Pseudo-knot forming internal loop
176IL_76486.11Sarcin-ricin motif with syn G
177IL_37990.11
178IL_82601.11Tandem cWW water-inserted CU pairs
179IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
180IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
181IL_06468.1116S h40 3WJ E.c.
182IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
183IL_97073.11
184IL_03931.1116S h19 IL and 23S H41 IL
185IL_54576.11
186IL_06306.11
187IL_97842.11
188IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
189IL_17603.11
190IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
191IL_91089.11
192IL_30067.11
193IL_85805.11
194IL_92280.11
195IL_02835.11
196IL_12507.11
197IL_47687.11
198IL_21221.11SSU Helix 12 (h12) IL
199IL_03741.11
200IL_83856.11
201IL_37347.11
202IL_46306.11
203IL_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.
204IL_15205.11
205IL_60643.11
206IL_52610.11
207IL_83250.1116S h40 3WJ T.th.
208IL_03110.11
209IL_80505.11
210IL_55649.11
211IL_52509.11
212IL_02690.11
213IL_91078.11
214IL_81398.11
215IL_05221.11
216IL_06471.11
217IL_91904.11
218IL_56513.11
219IL_91044.11
220IL_47732.11
221IL_63952.11
222IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
223IL_41791.11
224IL_43316.11
225IL_82650.11
226IL_26868.11
227IL_89794.11
228IL_95774.11tHS tHH bulge with S-turn
229IL_12486.11
230IL_71942.11
231IL_82113.11
232IL_53323.11
233IL_26971.11
234IL_09491.11
235IL_21421.11
236IL_85510.11
237IL_06847.11Group II Intron IL
238IL_30354.11
239IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
240IL_57977.11
241IL_39324.11
242IL_25307.11
243IL_11302.11
244IL_53988.11
245IL_28644.11
246IL_11778.11
247IL_37715.11
248IL_54450.11
249IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
250IL_25082.11
251IL_98924.11
252IL_59529.11
253IL_02957.11
254IL_28468.11Single sheared with bulged bases
255IL_88367.11
256IL_60649.11Kink-turn
257IL_46721.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription