Changes in PDB files used for clustering

Release 1.1 has 199 PDB files, release 1.2 has 200 PDB files, 199 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.2: 4JRC.

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 1.1 has 271 motif groups, release 1.2 has 271 motif groups, 268 of them are identical.

2 motif groups were updated, 1 groups are present only in release 1.1, 1 groups are only in release 1.2.

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_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_94430.41516S h32-h33-h34 3WJ
18IL_31555.315Tandem sheared with inserted, unpaired purine.
19IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
20IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_46648.21123S H91 IL | Single-Base Intercalation Site
22IL_40090.31116S h34 ILa : Part of larger motif
23IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
25IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_47444.39SRP Loop E-like motif
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_73000.27cHS-cWS
32IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_13069.36LSU 3WJ H32-H33-H35A
35IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36IL_70237.36
37IL_54420.16
38IL_25230.36Bacterial 5S rRNA Loop E
39IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
40IL_97057.36
41IL_53635.36LSU Helix 32 (H32) IL
42IL_90133.26
43IL_72158.36LSU Helix 62 (H62) IL
44IL_92484.15
45IL_82188.15LSU H68 IL from H.m.
46IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
47IL_79083.35
48IL_25300.1516S h19 IL and 23S H41 IL
49IL_45262.35
50IL_86357.35LSU Helix 61 IL2
51IL_16207.15Single sheared with bulged bases
52IL_02359.35
53IL_08926.2523S H91 IL
54IL_78732.35Double S-turn motif
55IL_77263.15Kink-turn from U4
56IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
57IL_01080.14
58IL_98591.34
59IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60IL_22732.14tSH-inserted-tHS
61IL_42251.14
62IL_38807.34
63IL_34363.24Kink-turn from 23S H42
64IL_08559.14LSU Helix 89 (H89) IL2
65IL_28572.1416S h18 kink-turn like motif
66IL_21333.24tSH-tHW-bulge
67IL_16166.3423S H91 IL
68IL_31066.24SSU Helix 44 (h44) extension
69IL_39526.44
70IL_80348.1323S H91 IL
71IL_52173.13
72IL_58586.23
73IL_34628.23Kink-turn
74IL_98421.33SSU Helix 12 (h12) IL
75IL_05723.13
76IL_56077.13
77IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
78IL_95150.33
79IL_80494.23LSU H58 IL2 H.m.
80IL_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.
81IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
82IL_79955.23SSU Helix (23) h23 IL1
83IL_37053.13Kink-turn from 23S H58
84IL_92267.1323S H73 ILa : Part of larger Motif
85IL_34156.63cWW AG or UU
86IL_75447.13
87IL_48918.23Kink-turn variant
88IL_62499.63
89IL_43946.13
90IL_82563.13Thi-box riboswitch T-loop
91IL_10647.13tHS tHH bulge with S-turn
92IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
93IL_30840.13
94IL_31707.12Vitamin B12 aptamer
95IL_76095.32Motif from Hairpin Ribozyme
96IL_21495.12
97IL_37406.12
98IL_69536.12LSU Helix 96 (H96) IL2
99IL_28942.12
100IL_40892.12
101IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
102IL_80093.12
103IL_01054.12
104IL_15840.22Triple Sheared with unpaired, inserted A
105IL_23262.42
106IL_49550.12tHS tHH bulge with S-turn
107IL_50521.12
108IL_70280.12Double sheared with wobble cWW.
109IL_88180.12cWW-bulge-cWW
110IL_87548.12
111IL_09882.12
112IL_77076.12
113IL_12211.12
114IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
115IL_55287.12
116IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
117IL_52940.12
118IL_90057.12
119IL_33925.12
120IL_00998.12
121IL_16252.3223S H91 IL
122IL_94744.12Sarcin-ricin motif with extra cWW GA pair
123IL_11751.12
124IL_65137.12Kink-turn like motif in Group I Intron
125IL_19898.12
126IL_91273.12
127IL_27892.12
128IL_23414.12
129IL_37197.12
130IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
131IL_98566.12
132IL_09587.12
133IL_07300.12
134IL_45794.12
135IL_33964.12
136IL_97833.12
137IL_46435.12
138IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
139IL_09901.12tHS tHH bulge with S-turn
140IL_24358.12
141IL_16330.12
142IL_02835.11
143IL_12507.11
144IL_47687.11
145IL_21221.11SSU Helix 12 (h12) IL
146IL_03741.11
147IL_83856.11
148IL_37347.11
149IL_46306.11
150IL_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.
151IL_15205.11
152IL_60643.11
153IL_52610.11
154IL_92280.11
155IL_03110.11
156IL_80505.11
157IL_55649.11
158IL_52509.11
159IL_02690.11
160IL_91078.11
161IL_81398.11
162IL_05221.11
163IL_06471.11
164IL_91904.11
165IL_56513.11
166IL_91044.11
167IL_47732.11
168IL_85805.11
169IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
170IL_41791.11
171IL_43316.11
172IL_82650.11
173IL_26868.11
174IL_89794.11
175IL_95774.11tHS tHH bulge with S-turn
176IL_12486.11
177IL_71942.11
178IL_82113.11
179IL_53323.11
180IL_26971.11
181IL_09491.11
182IL_21421.11
183IL_85510.11
184IL_06847.11Group II Intron IL
185IL_30354.11
186IL_83250.1116S h40 3WJ T.th.
187IL_57977.11
188IL_39324.11
189IL_25307.11
190IL_11302.11
191IL_53988.11
192IL_28644.11
193IL_11778.11
194IL_37715.11
195IL_54450.11
196IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
197IL_25082.11
198IL_98924.11
199IL_59529.11
200IL_02957.11
201IL_28468.11Single sheared with bulged bases
202IL_88367.11
203IL_60649.11Kink-turn
204IL_46721.11
205IL_63952.11
206IL_86059.11
207IL_04550.11tHS tHH bulge with S-turn
208IL_66744.11SSU Helix 21 (h21) IL2 E.coli
209IL_05462.11
210IL_20775.11tSH-inserted
211IL_13682.11
212IL_31290.11
213IL_13434.11
214IL_71685.11Sarcin-like with an intercalated basepair
215IL_25181.11
216IL_58454.11
217IL_40527.11Kink-turn
218IL_77296.11
219IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
220IL_06808.11Double sheared (tSH-tSH) one bulged base.
221IL_61730.11
222IL_67735.11
223IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
224IL_23639.11tWH-tHS-L-cWW
225IL_64589.11
226IL_41139.11
227IL_03282.11
228IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
229IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
230IL_83920.11
231IL_52958.11
232IL_80652.11
233IL_65788.11
234IL_78809.11
235IL_75415.11Pseudo-knot forming internal loop
236IL_76486.11Sarcin-ricin motif with syn G
237IL_37990.11
238IL_82601.11Tandem cWW water-inserted CU pairs
239IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
240IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
241IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
242IL_40845.11
243IL_06468.1116S h40 3WJ E.c.
244IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
245IL_97073.11
246IL_03931.1116S h19 IL and 23S H41 IL
247IL_54576.11
248IL_06306.11
249IL_97842.11
250IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
251IL_17603.11
252IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
253IL_91089.11
254IL_30067.11

Updated motif groups

#Motif idInstancesDescription
1IL_73276.321C-loop
2IL_71565.33

Removed motif groups

#Motif idInstancesDescription
1IL_89231.12LSU H77

Added motif groups

#Motif idInstancesDescription
1IL_94403.14LSU H77