Changes in PDB files used for clustering

Release 1.3 has 201 PDB files, release 1.4 has 202 PDB files, 201 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_46648.21123S H91 IL | Single-Base Intercalation Site
22IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
23IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_13069.36LSU 3WJ H32-H33-H35A
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
38IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
39IL_97057.36
40IL_53635.36LSU Helix 32 (H32) IL
41IL_90133.26
42IL_72158.36LSU Helix 62 (H62) IL
43IL_92484.15
44IL_25300.1516S h19 IL and 23S H41 IL
45IL_82188.15LSU H68 IL from H.m.
46IL_78732.35Double S-turn motif
47IL_02359.35
48IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
49IL_77263.15Kink-turn from U4
50IL_45262.35
51IL_86357.35LSU Helix 61 IL2
52IL_16207.15Single sheared with bulged bases
53IL_08926.2523S H91 IL
54IL_79083.35
55IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
56IL_98591.34
57IL_94403.14LSU H77
58IL_08559.14LSU Helix 89 (H89) IL2
59IL_39526.44
60IL_28572.1416S h18 kink-turn like motif
61IL_31066.24SSU Helix 44 (h44) extension
62IL_21333.24tSH-tHW-bulge
63IL_42251.14
64IL_38807.34
65IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
66IL_01080.14
67IL_16166.3423S H91 IL
68IL_34363.24Kink-turn from 23S H42
69IL_22732.14tSH-inserted-tHS
70IL_58586.23
71IL_82563.13Thi-box riboswitch T-loop
72IL_79955.23SSU Helix (23) h23 IL1
73IL_05723.13
74IL_62499.63
75IL_71565.33
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_30840.13
79IL_37053.13Kink-turn from 23S H58
80IL_92267.1323S H73 ILa : Part of larger Motif
81IL_48918.23Kink-turn variant
82IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
83IL_34156.63cWW AG or UU
84IL_10647.13tHS tHH bulge with S-turn
85IL_80348.1323S H91 IL
86IL_52173.13
87IL_43946.13
88IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
89IL_56077.13
90IL_34628.23Kink-turn
91IL_98421.33SSU Helix 12 (h12) IL
92IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
93IL_95150.33
94IL_75447.13
95IL_50521.12
96IL_09882.12
97IL_91273.12
98IL_00998.12
99IL_16252.3223S H91 IL
100IL_94744.12Sarcin-ricin motif with extra cWW GA pair
101IL_49550.12tHS tHH bulge with S-turn
102IL_96446.12
103IL_87548.12
104IL_52940.12
105IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
106IL_80093.12
107IL_46435.12
108IL_09587.12
109IL_27892.12
110IL_88180.12cWW-bulge-cWW
111IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
112IL_65137.12Kink-turn like motif in Group I Intron
113IL_77076.12
114IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
115IL_55287.12
116IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
117IL_11751.12
118IL_19898.12
119IL_90057.12
120IL_12211.12
121IL_21495.12
122IL_09901.12tHS tHH bulge with S-turn
123IL_33925.12
124IL_01054.12
125IL_15840.22Triple Sheared with unpaired, inserted A
126IL_37406.12
127IL_69536.12LSU Helix 96 (H96) IL2
128IL_28942.12
129IL_23414.12
130IL_37197.12
131IL_31707.12Vitamin B12 aptamer
132IL_97833.12
133IL_23262.42
134IL_07300.12
135IL_45794.12
136IL_33964.12
137IL_76095.32Motif from Hairpin Ribozyme
138IL_98566.12
139IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
140IL_70280.12Double sheared with wobble cWW.
141IL_24358.12
142IL_16330.12
143IL_40892.12
144IL_83250.1116S h40 3WJ T.th.
145IL_02835.11
146IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
147IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
148IL_05462.11
149IL_20775.11tSH-inserted
150IL_71942.11
151IL_91078.11
152IL_81398.11
153IL_05221.11
154IL_06471.11
155IL_91904.11
156IL_56513.11
157IL_60643.11
158IL_46721.11
159IL_03110.11
160IL_83920.11
161IL_06808.11Double sheared (tSH-tSH) one bulged base.
162IL_27243.11
163IL_75328.11
164IL_82113.11
165IL_53323.11
166IL_26971.11
167IL_09491.11
168IL_21421.11
169IL_85510.11
170IL_91044.11
171IL_27668.11
172IL_63952.11
173IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
174IL_41791.11
175IL_43316.11
176IL_12507.11
177IL_06468.1116S h40 3WJ E.c.
178IL_52958.11
179IL_80652.11
180IL_65788.11
181IL_61730.11
182IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
183IL_25082.11
184IL_98924.11
185IL_59529.11
186IL_02957.11
187IL_28468.11Single sheared with bulged bases
188IL_88367.11
189IL_06847.11Group II Intron IL
190IL_30067.11
191IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
192IL_57977.11
193IL_39324.11
194IL_80505.11
195IL_47687.11
196IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
197IL_97073.11
198IL_03931.1116S h19 IL and 23S H41 IL
199IL_78809.11
200IL_13682.11
201IL_31290.11
202IL_13434.11
203IL_71685.11Sarcin-like with an intercalated basepair
204IL_25181.11
205IL_58454.11
206IL_40527.11Kink-turn
207IL_60649.11Kink-turn
208IL_52610.11
209IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
210IL_86059.11
211IL_82650.11
212IL_31006.11tSH-tHW-L-bif-cWW
213IL_21221.11SSU Helix 12 (h12) IL
214IL_54576.11
215IL_67735.11
216IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
217IL_23639.11tWH-tHS-L-cWW
218IL_64589.11
219IL_41139.11
220IL_77296.11
221IL_87394.11
222IL_40845.11
223IL_25307.11
224IL_26868.11
225IL_55649.11
226IL_52509.11
227IL_02690.11
228IL_75415.11Pseudo-knot forming internal loop
229IL_76486.11Sarcin-ricin motif with syn G
230IL_37990.11
231IL_82601.11Tandem cWW water-inserted CU pairs
232IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
233IL_03282.11
234IL_42891.11
235IL_88865.11
236IL_76263.11
237IL_91379.11
238IL_11302.11
239IL_89794.11
240IL_95774.11tHS tHH bulge with S-turn
241IL_12486.11
242IL_06306.11
243IL_97842.11
244IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
245IL_17603.11
246IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
247IL_91089.11
248IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
249IL_47732.11
250IL_85805.11
251IL_92280.11
252IL_68827.11Reverse Kink-Turn
253IL_04550.11tHS tHH bulge with S-turn
254IL_66744.11SSU Helix 21 (h21) IL2 E.coli
255IL_53988.11
256IL_28644.11
257IL_11778.11
258IL_37715.11
259IL_54450.11
260IL_77014.11
261IL_03741.11
262IL_83856.11
263IL_37347.11
264IL_46306.11
265IL_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.
266IL_15205.11
267IL_23448.11
268IL_57285.11
269IL_30354.11

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