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

Loading the Sankey diagram...

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_65553.522Kink-turn
10IL_93424.322tSH-inserted-tHW
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_85647.316Sarcin-ricin parent motif with 15 Nts
16IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_94430.41516S h32-h33-h34 3WJ
19IL_31555.315Tandem sheared with inserted, unpaired purine.
20IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_46648.21123S H91 IL | Single-Base Intercalation Site
22IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
25IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
26IL_47444.39SRP Loop E-like motif
27IL_90459.39cWW AG or UU
28IL_92114.39GAAA loop receptor "platform" motif
29IL_58291.39Recurrent Sub-motif found in junctions
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_53635.36LSU Helix 32 (H32) IL
34IL_97057.36
35IL_90133.26
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
38IL_54420.16
39IL_13069.36LSU 3WJ H32-H33-H35A
40IL_72158.36LSU Helix 62 (H62) IL
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_70237.36
43IL_78732.35Double S-turn motif
44IL_86357.35LSU Helix 61 IL2
45IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
46IL_16207.15Single sheared with bulged bases
47IL_79083.35
48IL_08926.2523S H91 IL
49IL_25300.1516S h19 IL and 23S H41 IL
50IL_45262.35
51IL_82188.15LSU H68 IL from H.m.
52IL_77263.15Kink-turn from U4
53IL_92484.15
54IL_02359.35
55IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
56IL_98591.34
57IL_22732.14tSH-inserted-tHS
58IL_31066.24SSU Helix 44 (h44) extension
59IL_34363.24Kink-turn from 23S H42
60IL_94403.14LSU H77
61IL_16166.3423S H91 IL
62IL_28572.1416S h18 kink-turn like motif
63IL_38807.34
64IL_08559.14LSU Helix 89 (H89) IL2
65IL_39526.44
66IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
67IL_01080.14
68IL_21333.24tSH-tHW-bulge
69IL_42251.14
70IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
71IL_30840.13
72IL_34156.63cWW AG or UU
73IL_58586.23
74IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
75IL_43946.13
76IL_56077.13
77IL_34628.23Kink-turn
78IL_52173.13
79IL_71565.33
80IL_75447.13
81IL_05723.13
82IL_92267.1323S H73 ILa : Part of larger Motif
83IL_10647.13tHS tHH bulge with S-turn
84IL_37053.13Kink-turn from 23S H58
85IL_79955.23SSU Helix (23) h23 IL1
86IL_82563.13Thi-box riboswitch T-loop
87IL_95150.33
88IL_48918.23Kink-turn variant
89IL_62499.63
90IL_80348.1323S H91 IL
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_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
93IL_98421.33SSU Helix 12 (h12) IL
94IL_80494.23LSU H58 IL2 H.m.
95IL_12211.12
96IL_21495.12
97IL_27892.12
98IL_49550.12tHS tHH bulge with S-turn
99IL_70280.12Double sheared with wobble cWW.
100IL_90057.12
101IL_09587.12
102IL_15840.22Triple Sheared with unpaired, inserted A
103IL_19898.12
104IL_40892.12
105IL_50521.12
106IL_65137.12Kink-turn like motif in Group I Intron
107IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
108IL_07300.12
109IL_09882.12
110IL_23262.42
111IL_87548.12
112IL_09901.12tHS tHH bulge with S-turn
113IL_23414.12
114IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
115IL_76095.32Motif from Hairpin Ribozyme
116IL_94744.12Sarcin-ricin motif with extra cWW GA pair
117IL_00998.12
118IL_16252.3223S H91 IL
119IL_28942.12
120IL_31707.12Vitamin B12 aptamer
121IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
122IL_88180.12cWW-bulge-cWW
123IL_97833.12
124IL_01054.12
125IL_16330.12
126IL_24358.12
127IL_37197.12
128IL_45794.12
129IL_52940.12
130IL_77076.12
131IL_80093.12
132IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
133IL_11751.12
134IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
135IL_33925.12
136IL_55287.12
137IL_69536.12LSU Helix 96 (H96) IL2
138IL_91273.12
139IL_33964.12
140IL_37406.12
141IL_46435.12
142IL_98566.12
143IL_02690.11
144IL_04550.11tHS tHH bulge with S-turn
145IL_06808.11Double sheared (tSH-tSH) one bulged base.
146IL_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.
147IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
148IL_25082.11
149IL_37715.11
150IL_40845.11
151IL_43316.11
152IL_64589.11
153IL_80505.11
154IL_83250.1116S h40 3WJ T.th.
155IL_05221.11
156IL_06847.11Group II Intron IL
157IL_12486.11
158IL_25181.11
159IL_28468.11Single sheared with bulged bases
160IL_37990.11
161IL_46721.11
162IL_53988.11
163IL_59529.11
164IL_75415.11Pseudo-knot forming internal loop
165IL_80652.11
166IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
167IL_97073.11
168IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
169IL_02835.11
170IL_05462.11
171IL_12507.11
172IL_20775.11tSH-inserted
173IL_31290.11
174IL_41139.11
175IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
176IL_78809.11
177IL_81398.11
178IL_83856.11
179IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
180IL_98924.11
181IL_02957.11
182IL_21221.11SSU Helix 12 (h12) IL
183IL_28644.11
184IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
185IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
186IL_47687.11
187IL_52509.11
188IL_54450.11
189IL_56513.11
190IL_60643.11
191IL_65788.11
192IL_71685.11Sarcin-like with an intercalated basepair
193IL_82113.11
194IL_83920.11
195IL_91044.11
196IL_03110.11
197IL_06306.11
198IL_13434.11
199IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
200IL_23639.11tWH-tHS-L-cWW
201IL_39324.11
202IL_47732.11
203IL_52610.11
204IL_54576.11
205IL_60649.11Kink-turn
206IL_66744.11SSU Helix 21 (h21) IL2 E.coli
207IL_71942.11
208IL_76486.11Sarcin-ricin motif with syn G
209IL_85510.11
210IL_91078.11
211IL_92280.11
212IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
213IL_03282.11
214IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
215IL_11302.11
216IL_13682.11
217IL_25307.11
218IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
219IL_41791.11
220IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
221IL_57977.11
222IL_61730.11
223IL_67735.11
224IL_88367.11
225IL_91089.11
226IL_97842.11
227IL_03741.11
228IL_06468.1116S h40 3WJ E.c.
229IL_26868.11
230IL_30067.11
231IL_37347.11
232IL_46306.11
233IL_52958.11
234IL_82601.11Tandem cWW water-inserted CU pairs
235IL_85805.11
236IL_03931.1116S h19 IL and 23S H41 IL
237IL_06471.11
238IL_09491.11
239IL_11778.11
240IL_15205.11
241IL_17603.11
242IL_21421.11
243IL_26971.11
244IL_30354.11
245IL_40527.11Kink-turn
246IL_53323.11
247IL_55649.11
248IL_58454.11
249IL_63952.11
250IL_77296.11
251IL_82650.11
252IL_86059.11
253IL_89794.11
254IL_91904.11
255IL_95774.11tHS tHH bulge with S-turn

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