Changes in PDB files used for clustering

Release 1.5 has 203 PDB files, release 1.6 has 203 PDB files, 202 of them are identical.

1 equivalence classes changed representatives: 3NPB4KQY.

No new PDB files have been added.

Obsolete: 3NPB4KQY.

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 1.5 has 274 motif groups, release 1.6 has 272 motif groups, 254 of them are identical.

6 motif groups were updated, 14 groups are present only in release 1.5, 12 groups are only in release 1.6.

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_97217.72431-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.8205cWW AG or water inserted cWW Y-Y.
3IL_39199.453Hoogsteen-edge Platform, Single bulged base
4IL_41766.449Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.443Sugar-edge, 1-base platform, consensus tHS
7IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_82444.129cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
9IL_13959.426Double Sheared (tSH-tHS)
10IL_93424.421tSH-inserted-tHW
11IL_73276.421C-loop
12IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
13IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.31716S h21 S8 binding site
15IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_94430.51616S h32-h33-h34 3WJ
17IL_85647.316Sarcin-ricin parent motif with 15 Nts
18IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
19IL_31555.413Tandem sheared with inserted, unpaired purine.
20IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_58291.410Recurrent Sub-motif found in junctions
23IL_47444.39SRP Loop E-like motif
24IL_90459.39cWW AG or UU
25IL_92114.39GAAA loop receptor "platform" motif
26IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
27IL_73000.27cHS-cWS
28IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
29IL_13069.36LSU 3WJ H32-H33-H35A
30IL_25380.16LSU Helix 89 (H89) IL2
31IL_53635.36LSU Helix 32 (H32) IL
32IL_72158.36LSU Helix 62 (H62) IL
33IL_77263.26Kink-turn from U4
34IL_97057.36
35IL_08926.3623S H91 IL
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
38IL_70237.36
39IL_90133.36
40IL_86357.35LSU Helix 61 IL2
41IL_79083.35
42IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
43IL_25300.1516S h19 IL and 23S H41 IL
44IL_02359.35
45IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
46IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47IL_09530.14Double S-turn motif
48IL_21333.24tSH-tHW-bulge
49IL_34363.24Kink-turn from 23S H42
50IL_45262.44
51IL_98591.34
52IL_31066.34SSU Helix 44 (h44) extension
53IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
54IL_28572.2416S h18 kink-turn like motif
55IL_39526.44
56IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
57IL_22732.14tSH-inserted-tHS
58IL_42251.14
59IL_82188.24LSU H68 IL from H.m.
60IL_31663.1423S H73 ILa : Part of larger Motif
61IL_39980.14
62IL_01080.14
63IL_38807.34
64IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
65IL_05723.13
66IL_80494.23LSU H58 IL2 H.m.
67IL_30840.23
68IL_06180.13tHS tHH bulge with S-turn
69IL_07300.23
70IL_34628.23Kink-turn
71IL_52173.13
72IL_89028.63Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
73IL_06211.13
74IL_37053.13Kink-turn from 23S H58
75IL_62499.73
76IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
77IL_87065.1323S H91 IL | Single-Base Intercalation Site
78IL_48918.23Kink-turn variant
79IL_16166.4323S H91 IL
80IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
81IL_75447.13
82IL_79955.23SSU Helix (23) h23 IL1
83IL_43946.13
84IL_58586.23
85IL_82563.13Thi-box riboswitch T-loop
86IL_95150.43
87IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
88IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
89IL_80348.1323S H91 IL
90IL_98421.43SSU Helix 12 (h12) IL
91IL_30381.12tHS tHH bulge with S-turn
92IL_33964.12
93IL_40892.12
94IL_50521.12
95IL_67887.12
96IL_77076.12
97IL_96206.12
98IL_98566.12
99IL_09587.12
100IL_09882.12
101IL_21495.12
102IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
103IL_45794.12
104IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
105IL_69536.12LSU Helix 96 (H96) IL2
106IL_19898.12
107IL_21639.12
108IL_46034.12
109IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
110IL_00998.12
111IL_11751.12
112IL_15840.22Triple Sheared with unpaired, inserted A
113IL_37197.12
114IL_87507.12tHS tHH bulge with S-turn
115IL_90057.12
116IL_94744.12Sarcin-ricin motif with extra cWW GA pair
117IL_97509.12Double sheared with wobble cWW.
118IL_01054.12
119IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
120IL_23262.42
121IL_46435.12
122IL_52940.12
123IL_97833.12
124IL_12211.12
125IL_16330.12
126IL_23414.12
127IL_31707.12Vitamin B12 aptamer
128IL_37406.12
129IL_65137.12Kink-turn like motif in Group I Intron
130IL_76095.32Motif from Hairpin Ribozyme
131IL_80093.12
132IL_87548.12
133IL_90735.12
134IL_02835.11
135IL_06808.11Double sheared (tSH-tSH) one bulged base.
136IL_17603.11
137IL_56513.11
138IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
139IL_82650.11
140IL_86059.11
141IL_88119.11
142IL_91044.11
143IL_02897.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
144IL_06177.11cWW AG or UU
145IL_06847.11Group II Intron IL
146IL_13682.11
147IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
148IL_21421.11
149IL_26868.11
150IL_39324.11
151IL_41139.11
152IL_47687.11
153IL_50911.1116S h34 ILa : Part of larger motif
154IL_53988.11
155IL_57364.11LSU Helix 89 (H89) IL2
156IL_60649.11Kink-turn
157IL_68767.11
158IL_80505.11
159IL_83250.1116S h40 3WJ T.th.
160IL_88367.11
161IL_91078.11
162IL_02957.11
163IL_18675.11cWW-bulge-cWW
164IL_25082.11
165IL_26971.11
166IL_47732.11
167IL_54450.11
168IL_61730.11
169IL_77296.11
170IL_80652.11
171IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
172IL_91089.11
173IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
174IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
175IL_03110.11
176IL_11302.11
177IL_15205.11
178IL_25181.11
179IL_31224.1123S H91 IL
180IL_41791.11
181IL_52509.11
182IL_54470.11tHS tHH bulge with S-turn
183IL_57977.11
184IL_69799.11
185IL_81398.11
186IL_83856.11
187IL_89794.11
188IL_91904.11
189IL_98924.11
190IL_03282.11
191IL_06306.11
192IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
193IL_20530.11
194IL_28644.11
195IL_46306.11
196IL_52610.11
197IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
198IL_63952.11
199IL_75415.11Pseudo-knot forming internal loop
200IL_83920.11
201IL_03741.11
202IL_06421.11Single sheared with bulged bases
203IL_11778.11
204IL_20775.11tSH-inserted
205IL_37347.11
206IL_43316.11
207IL_55649.11
208IL_58454.11
209IL_64589.11
210IL_85510.11
211IL_87523.11
212IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
213IL_05221.11
214IL_06468.1116S h40 3WJ E.c.
215IL_09491.11
216IL_21077.11
217IL_30067.11
218IL_40527.11Kink-turn
219IL_46721.11
220IL_49527.11
221IL_52958.11
222IL_71685.11Sarcin-like with an intercalated basepair
223IL_97842.11
224IL_06471.11
225IL_12507.11
226IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
227IL_23639.11tWH-tHS-L-cWW
228IL_25307.11
229IL_30354.11
230IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
231IL_40845.11
232IL_49976.11
233IL_53323.11
234IL_59529.11
235IL_66744.11SSU Helix 21 (h21) IL2 E.coli
236IL_71942.11
237IL_76486.11Sarcin-ricin motif with syn G
238IL_82601.11Tandem cWW water-inserted CU pairs
239IL_85805.11
240IL_92280.11

Updated motif groups

#Motif idInstancesDescription
1IL_65553.722Kink-turn
2IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
4IL_46648.41123S H91 IL | Single-Base Intercalation Site
5IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
6IL_94403.34LSU H77

Removed motif groups

#Motif idInstancesDescription
1IL_40090.510Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
2IL_15768.14cWW AG or UU | cWH basepair with syn base
3IL_71565.44
4IL_55287.12
5IL_12685.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6IL_35595.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases
7IL_35994.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
8IL_37990.11
9IL_96182.11cWH basepair with syn base
10IL_99438.11
11IL_54576.11
12IL_59018.11
13IL_60643.11
14IL_78809.11

Added motif groups

#Motif idInstancesDescription
1IL_17212.110cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
2IL_15709.14Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
4IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
5IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6IL_80433.12
7IL_85015.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
8IL_41153.11
9IL_10365.11
10IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
11IL_25314.11
12IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW