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_73276.421C-loop
11IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
12IL_93424.421tSH-inserted-tHW
13IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.31716S h21 S8 binding site
15IL_94430.51616S h32-h33-h34 3WJ
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
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_58291.410Recurrent Sub-motif found in junctions
22IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_90459.39cWW AG or UU
24IL_92114.39GAAA loop receptor "platform" motif
25IL_47444.39SRP Loop E-like motif
26IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
27IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28IL_73000.27cHS-cWS
29IL_08926.3623S H91 IL
30IL_25230.36Bacterial 5S rRNA Loop E
31IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
32IL_70237.36
33IL_90133.36
34IL_25380.16LSU Helix 89 (H89) IL2
35IL_53635.36LSU Helix 32 (H32) IL
36IL_72158.36LSU Helix 62 (H62) IL
37IL_13069.36LSU 3WJ H32-H33-H35A
38IL_77263.26Kink-turn from U4
39IL_97057.36
40IL_79083.35
41IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
42IL_25300.1516S h19 IL and 23S H41 IL
43IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
44IL_02359.35
45IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
46IL_86357.35LSU Helix 61 IL2
47IL_31066.34SSU Helix 44 (h44) extension
48IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
49IL_28572.2416S h18 kink-turn like motif
50IL_39526.44
51IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
52IL_22732.14tSH-inserted-tHS
53IL_42251.14
54IL_82188.24LSU H68 IL from H.m.
55IL_31663.1423S H73 ILa : Part of larger Motif
56IL_39980.14
57IL_01080.14
58IL_38807.34
59IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
60IL_21333.24tSH-tHW-bulge
61IL_09530.14Double S-turn motif
62IL_34363.24Kink-turn from 23S H42
63IL_45262.44
64IL_98591.34
65IL_34628.23Kink-turn
66IL_52173.13
67IL_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.
68IL_06180.13tHS tHH bulge with S-turn
69IL_07300.23
70IL_37053.13Kink-turn from 23S H58
71IL_62499.73
72IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
73IL_87065.1323S H91 IL | Single-Base Intercalation Site
74IL_06211.13
75IL_48918.23Kink-turn variant
76IL_16166.4323S H91 IL
77IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
78IL_75447.13
79IL_79955.23SSU Helix (23) h23 IL1
80IL_43946.13
81IL_58586.23
82IL_82563.13Thi-box riboswitch T-loop
83IL_95150.43
84IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
85IL_80348.1323S H91 IL
86IL_98421.43SSU Helix 12 (h12) IL
87IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
88IL_80494.23LSU H58 IL2 H.m.
89IL_05723.13
90IL_30840.23
91IL_21495.12
92IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
93IL_45794.12
94IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
95IL_69536.12LSU Helix 96 (H96) IL2
96IL_09882.12
97IL_19898.12
98IL_21639.12
99IL_46034.12
100IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
101IL_15840.22Triple Sheared with unpaired, inserted A
102IL_37197.12
103IL_87507.12tHS tHH bulge with S-turn
104IL_90057.12
105IL_94744.12Sarcin-ricin motif with extra cWW GA pair
106IL_97509.12Double sheared with wobble cWW.
107IL_00998.12
108IL_11751.12
109IL_23262.42
110IL_46435.12
111IL_52940.12
112IL_97833.12
113IL_01054.12
114IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
115IL_16330.12
116IL_23414.12
117IL_31707.12Vitamin B12 aptamer
118IL_37406.12
119IL_65137.12Kink-turn like motif in Group I Intron
120IL_76095.32Motif from Hairpin Ribozyme
121IL_80093.12
122IL_87548.12
123IL_12211.12
124IL_90735.12
125IL_30381.12tHS tHH bulge with S-turn
126IL_33964.12
127IL_40892.12
128IL_50521.12
129IL_67887.12
130IL_77076.12
131IL_96206.12
132IL_98566.12
133IL_09587.12
134IL_18675.11cWW-bulge-cWW
135IL_25082.11
136IL_26971.11
137IL_47732.11
138IL_54450.11
139IL_61730.11
140IL_77296.11
141IL_80652.11
142IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
143IL_91089.11
144IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
145IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
146IL_02957.11
147IL_15205.11
148IL_25181.11
149IL_31224.1123S H91 IL
150IL_41791.11
151IL_52509.11
152IL_54470.11tHS tHH bulge with S-turn
153IL_57977.11
154IL_69799.11
155IL_81398.11
156IL_83856.11
157IL_89794.11
158IL_91904.11
159IL_98924.11
160IL_03110.11
161IL_11302.11
162IL_20530.11
163IL_28644.11
164IL_46306.11
165IL_52610.11
166IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
167IL_63952.11
168IL_75415.11Pseudo-knot forming internal loop
169IL_83920.11
170IL_03282.11
171IL_06306.11
172IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
173IL_20775.11tSH-inserted
174IL_37347.11
175IL_43316.11
176IL_55649.11
177IL_58454.11
178IL_64589.11
179IL_85510.11
180IL_87523.11
181IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
182IL_03741.11
183IL_06421.11Single sheared with bulged bases
184IL_11778.11
185IL_21077.11
186IL_30067.11
187IL_40527.11Kink-turn
188IL_46721.11
189IL_49527.11
190IL_52958.11
191IL_71685.11Sarcin-like with an intercalated basepair
192IL_97842.11
193IL_05221.11
194IL_06468.1116S h40 3WJ E.c.
195IL_09491.11
196IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
197IL_23639.11tWH-tHS-L-cWW
198IL_25307.11
199IL_30354.11
200IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
201IL_40845.11
202IL_49976.11
203IL_53323.11
204IL_59529.11
205IL_66744.11SSU Helix 21 (h21) IL2 E.coli
206IL_71942.11
207IL_76486.11Sarcin-ricin motif with syn G
208IL_82601.11Tandem cWW water-inserted CU pairs
209IL_85805.11
210IL_92280.11
211IL_06471.11
212IL_12507.11
213IL_17603.11
214IL_56513.11
215IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
216IL_82650.11
217IL_86059.11
218IL_88119.11
219IL_91044.11
220IL_02835.11
221IL_06808.11Double sheared (tSH-tSH) one bulged base.
222IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
223IL_21421.11
224IL_26868.11
225IL_39324.11
226IL_41139.11
227IL_47687.11
228IL_50911.1116S h34 ILa : Part of larger motif
229IL_53988.11
230IL_57364.11LSU Helix 89 (H89) IL2
231IL_60649.11Kink-turn
232IL_68767.11
233IL_80505.11
234IL_83250.1116S h40 3WJ T.th.
235IL_88367.11
236IL_91078.11
237IL_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.
238IL_06177.11cWW AG or UU
239IL_06847.11Group II Intron IL
240IL_13682.11

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_35595.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases
5IL_35994.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
6IL_55287.12
7IL_12685.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
8IL_60643.11
9IL_78809.11
10IL_37990.11
11IL_96182.11cWH basepair with syn base
12IL_99438.11
13IL_54576.11
14IL_59018.11

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_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)
6IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
7IL_80433.12
8IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
9IL_25314.11
10IL_97095.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
11IL_41153.11
12IL_10365.11