Changes in PDB files used for clustering

Release 1.3 has 200 PDB files, release 1.4 has 201 PDB files, 200 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.4: 4KYY.

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 1.3 has 271 motif groups, release 1.4 has 271 motif groups, 269 of them are identical.

2 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.

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_39199.354Hoogsteen-edge Platform, Single bulged base
3IL_41766.349Tandem cWW pairs (Not AU or GC)
4IL_56465.346Single, unpaired intercalated base, consensus A
5IL_44540.343Sugar-edge, 1-base platform, consensus tHS
6IL_87904.431Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_06390.326cWH basepair with syn base
8IL_13959.324Double Sheared (tSH-tHS)
9IL_93424.322tSH-inserted-tHW
10IL_65553.522Kink-turn
11IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
12IL_73276.321C-loop
13IL_55938.318LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.31716S h21 S8 binding site
15IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_31555.315Tandem sheared with inserted, unpaired purine.
18IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
19IL_94430.41516S h32-h33-h34 3WJ
20IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
23IL_46648.21123S H91 IL | Single-Base Intercalation Site
24IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
25IL_47444.39SRP Loop E-like motif
26IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_92114.39GAAA loop receptor "platform" motif
28IL_58291.39Recurrent Sub-motif found in junctions
29IL_90459.39cWW AG or UU
30IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_73000.27cHS-cWS
33IL_54420.16
34IL_70237.36
35IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
38IL_97057.36
39IL_53635.36LSU Helix 32 (H32) IL
40IL_90133.26
41IL_72158.36LSU Helix 62 (H62) IL
42IL_13069.36LSU 3WJ H32-H33-H35A
43IL_82188.15LSU H68 IL from H.m.
44IL_25300.1516S h19 IL and 23S H41 IL
45IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
46IL_79083.35
47IL_45262.35
48IL_77263.15Kink-turn from U4
49IL_86357.35LSU Helix 61 IL2
50IL_16207.15Single sheared with bulged bases
51IL_02359.35
52IL_08926.2523S H91 IL
53IL_78732.35Double S-turn motif
54IL_92484.15
55IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
56IL_94403.14LSU H77
57IL_42251.14
58IL_38807.34
59IL_28572.1416S h18 kink-turn like motif
60IL_31066.24SSU Helix 44 (h44) extension
61IL_21333.24tSH-tHW-bulge
62IL_34363.24Kink-turn from 23S H42
63IL_08559.14LSU Helix 89 (H89) IL2
64IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
65IL_01080.14
66IL_16166.3423S H91 IL
67IL_39526.44
68IL_22732.14tSH-inserted-tHS
69IL_98591.34
70IL_05723.13
71IL_56077.13
72IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
73IL_79955.23SSU Helix (23) h23 IL1
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_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
77IL_62499.63
78IL_71565.33
79IL_37053.13Kink-turn from 23S H58
80IL_92267.1323S H73 ILa : Part of larger Motif
81IL_34156.63cWW AG or UU
82IL_75447.13
83IL_48918.23Kink-turn variant
84IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
85IL_43946.13
86IL_82563.13Thi-box riboswitch T-loop
87IL_10647.13tHS tHH bulge with S-turn
88IL_80348.1323S H91 IL
89IL_52173.13
90IL_30840.13
91IL_98421.33SSU Helix 12 (h12) IL
92IL_95150.33
93IL_58586.23
94IL_34628.23Kink-turn
95IL_50521.12
96IL_09882.12
97IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
98IL_80093.12
99IL_01054.12
100IL_15840.22Triple Sheared with unpaired, inserted A
101IL_23262.42
102IL_49550.12tHS tHH bulge with S-turn
103IL_87548.12
104IL_52940.12
105IL_70280.12Double sheared with wobble cWW.
106IL_88180.12cWW-bulge-cWW
107IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
108IL_65137.12Kink-turn like motif in Group I Intron
109IL_77076.12
110IL_12211.12
111IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
112IL_55287.12
113IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
114IL_11751.12
115IL_19898.12
116IL_90057.12
117IL_33925.12
118IL_00998.12
119IL_16252.3223S H91 IL
120IL_94744.12Sarcin-ricin motif with extra cWW GA pair
121IL_91273.12
122IL_27892.12
123IL_23414.12
124IL_37197.12
125IL_31707.12Vitamin B12 aptamer
126IL_97833.12
127IL_98566.12
128IL_09587.12
129IL_07300.12
130IL_45794.12
131IL_33964.12
132IL_76095.32Motif from Hairpin Ribozyme
133IL_46435.12
134IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
135IL_09901.12tHS tHH bulge with S-turn
136IL_24358.12
137IL_16330.12
138IL_21495.12
139IL_37406.12
140IL_69536.12LSU Helix 96 (H96) IL2
141IL_28942.12
142IL_40892.12
143IL_83250.1116S h40 3WJ T.th.
144IL_03110.11
145IL_80505.11
146IL_55649.11
147IL_52509.11
148IL_02690.11
149IL_91078.11
150IL_81398.11
151IL_05221.11
152IL_06471.11
153IL_91904.11
154IL_56513.11
155IL_91044.11
156IL_47732.11
157IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
158IL_41791.11
159IL_43316.11
160IL_82650.11
161IL_26868.11
162IL_89794.11
163IL_95774.11tHS tHH bulge with S-turn
164IL_12486.11
165IL_71942.11
166IL_82113.11
167IL_53323.11
168IL_26971.11
169IL_09491.11
170IL_21421.11
171IL_85510.11
172IL_06847.11Group II Intron IL
173IL_30354.11
174IL_63952.11
175IL_57977.11
176IL_39324.11
177IL_25307.11
178IL_11302.11
179IL_53988.11
180IL_28644.11
181IL_11778.11
182IL_37715.11
183IL_54450.11
184IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
185IL_25082.11
186IL_98924.11
187IL_59529.11
188IL_02957.11
189IL_28468.11Single sheared with bulged bases
190IL_88367.11
191IL_60649.11Kink-turn
192IL_46721.11
193IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
194IL_86059.11
195IL_04550.11tHS tHH bulge with S-turn
196IL_66744.11SSU Helix 21 (h21) IL2 E.coli
197IL_05462.11
198IL_20775.11tSH-inserted
199IL_13682.11
200IL_31290.11
201IL_13434.11
202IL_71685.11Sarcin-like with an intercalated basepair
203IL_25181.11
204IL_58454.11
205IL_40527.11Kink-turn
206IL_77296.11
207IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
208IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
209IL_06808.11Double sheared (tSH-tSH) one bulged base.
210IL_61730.11
211IL_67735.11
212IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
213IL_23639.11tWH-tHS-L-cWW
214IL_64589.11
215IL_41139.11
216IL_03282.11
217IL_40845.11
218IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
219IL_83920.11
220IL_52958.11
221IL_80652.11
222IL_65788.11
223IL_78809.11
224IL_75415.11Pseudo-knot forming internal loop
225IL_76486.11Sarcin-ricin motif with syn G
226IL_37990.11
227IL_82601.11Tandem cWW water-inserted CU pairs
228IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
229IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
230IL_06468.1116S h40 3WJ E.c.
231IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
232IL_97073.11
233IL_03931.1116S h19 IL and 23S H41 IL
234IL_54576.11
235IL_06306.11
236IL_97842.11
237IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
238IL_17603.11
239IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
240IL_91089.11
241IL_30067.11
242IL_85805.11
243IL_92280.11
244IL_02835.11
245IL_12507.11
246IL_47687.11
247IL_21221.11SSU Helix 12 (h12) IL
248IL_03741.11
249IL_83856.11
250IL_37347.11
251IL_46306.11
252IL_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.
253IL_15205.11
254IL_60643.11
255IL_52610.11

Updated motif groups

#Motif idInstancesDescription
1IL_47174.7203cWW AG or water inserted cWW Y-Y.
2IL_40090.41216S h34 ILa : Part of larger motif

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription