Changes in PDB files used for clustering

Release 1.5 has 204 PDB files, release 1.6 has 204 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.6: 4KQY.

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_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
11IL_93424.421tSH-inserted-tHW
12IL_73276.421C-loop
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_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_25230.36Bacterial 5S rRNA Loop E
30IL_53635.36LSU Helix 32 (H32) IL
31IL_90133.36
32IL_72158.36LSU Helix 62 (H62) IL
33IL_13069.36LSU 3WJ H32-H33-H35A
34IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35IL_77263.26Kink-turn from U4
36IL_25380.16LSU Helix 89 (H89) IL2
37IL_70237.36
38IL_97057.36
39IL_08926.3623S H91 IL
40IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
41IL_79083.35
42IL_02359.35
43IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
44IL_25300.1516S h19 IL and 23S H41 IL
45IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
46IL_86357.35LSU Helix 61 IL2
47IL_21333.24tSH-tHW-bulge
48IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
49IL_39980.14
50IL_98591.34
51IL_09530.14Double S-turn motif
52IL_28572.2416S h18 kink-turn like motif
53IL_31066.34SSU Helix 44 (h44) extension
54IL_82188.24LSU H68 IL from H.m.
55IL_39526.44
56IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
57IL_01080.14
58IL_31663.1423S H73 ILa : Part of larger Motif
59IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60IL_22732.14tSH-inserted-tHS
61IL_38807.34
62IL_45262.44
63IL_42251.14
64IL_34363.24Kink-turn from 23S H42
65IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
66IL_16166.4323S H91 IL
67IL_75447.13
68IL_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.
69IL_34628.23Kink-turn
70IL_07300.23
71IL_62499.73
72IL_82563.13Thi-box riboswitch T-loop
73IL_87065.1323S H91 IL | Single-Base Intercalation Site
74IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
75IL_48918.23Kink-turn variant
76IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
77IL_52173.13
78IL_58586.23
79IL_05723.13
80IL_80348.1323S H91 IL
81IL_80494.23LSU H58 IL2 H.m.
82IL_98421.43SSU Helix 12 (h12) IL
83IL_37053.13Kink-turn from 23S H58
84IL_06180.13tHS tHH bulge with S-turn
85IL_06211.13
86IL_43946.13
87IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
88IL_30840.23
89IL_79955.23SSU Helix (23) h23 IL1
90IL_95150.43
91IL_87548.12
92IL_52940.12
93IL_98566.12
94IL_30381.12tHS tHH bulge with S-turn
95IL_67887.12
96IL_21639.12
97IL_37197.12
98IL_96446.12
99IL_11751.12
100IL_65137.12Kink-turn like motif in Group I Intron
101IL_97833.12
102IL_00998.12
103IL_45794.12
104IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
105IL_76095.32Motif from Hairpin Ribozyme
106IL_46435.12
107IL_09587.12
108IL_16330.12
109IL_87507.12tHS tHH bulge with S-turn
110IL_80093.12
111IL_97509.12Double sheared with wobble cWW.
112IL_40892.12
113IL_33964.12
114IL_31707.12Vitamin B12 aptamer
115IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
116IL_12211.12
117IL_21495.12
118IL_37406.12
119IL_90735.12
120IL_09882.12
121IL_77076.12
122IL_01054.12
123IL_15840.22Triple Sheared with unpaired, inserted A
124IL_94744.12Sarcin-ricin motif with extra cWW GA pair
125IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
126IL_90057.12
127IL_96206.12
128IL_23262.42
129IL_69536.12LSU Helix 96 (H96) IL2
130IL_23414.12
131IL_50521.12
132IL_19898.12
133IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
134IL_46034.12
135IL_68827.11Reverse Kink-Turn
136IL_66744.11SSU Helix 21 (h21) IL2 E.coli
137IL_53988.11
138IL_71685.11Sarcin-like with an intercalated basepair
139IL_02957.11
140IL_18675.11cWW-bulge-cWW
141IL_40527.11Kink-turn
142IL_23448.11
143IL_46721.11
144IL_63952.11
145IL_88865.11
146IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
147IL_83920.11
148IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
149IL_11778.11
150IL_03741.11
151IL_06306.11
152IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
153IL_23639.11tWH-tHS-L-cWW
154IL_57364.11LSU Helix 89 (H89) IL2
155IL_41139.11
156IL_91044.11
157IL_27668.11
158IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
159IL_02835.11
160IL_06421.11Single sheared with bulged bases
161IL_20775.11tSH-inserted
162IL_77014.11
163IL_91078.11
164IL_83856.11
165IL_76486.11Sarcin-ricin motif with syn G
166IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
167IL_64589.11
168IL_54470.11tHS tHH bulge with S-turn
169IL_06847.11Group II Intron IL
170IL_30067.11
171IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
172IL_40845.11
173IL_92280.11
174IL_03110.11
175IL_43316.11
176IL_12507.11
177IL_06468.1116S h40 3WJ E.c.
178IL_52958.11
179IL_06808.11Double sheared (tSH-tSH) one bulged base.
180IL_71942.11
181IL_81398.11
182IL_97842.11
183IL_46306.11
184IL_82601.11Tandem cWW water-inserted CU pairs
185IL_91089.11
186IL_60649.11Kink-turn
187IL_52610.11
188IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
189IL_41791.11
190IL_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.
191IL_80505.11
192IL_69799.11
193IL_47687.11
194IL_80652.11
195IL_54450.11
196IL_75328.11
197IL_20530.11
198IL_37347.11
199IL_06471.11
200IL_68767.11
201IL_17603.11
202IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
203IL_87523.11
204IL_77296.11
205IL_87394.11
206IL_50911.1116S h34 ILa : Part of larger motif
207IL_39324.11
208IL_06177.11cWW AG or UU
209IL_82650.11
210IL_31006.11tSH-tHW-L-bif-cWW
211IL_55649.11
212IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
213IL_13682.11
214IL_31224.1123S H91 IL
215IL_05221.11
216IL_26971.11
217IL_56513.11
218IL_15205.11
219IL_21077.11
220IL_03282.11
221IL_42891.11
222IL_85805.11
223IL_57977.11
224IL_86059.11
225IL_25307.11
226IL_26868.11
227IL_27243.11
228IL_25082.11
229IL_53323.11
230IL_59529.11
231IL_91904.11
232IL_21421.11
233IL_85510.11
234IL_49527.11
235IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
236IL_47732.11
237IL_83250.1116S h40 3WJ T.th.
238IL_76263.11
239IL_91379.11
240IL_11302.11
241IL_89794.11
242IL_28644.11
243IL_52509.11
244IL_61730.11
245IL_75415.11Pseudo-knot forming internal loop
246IL_88119.11
247IL_98924.11
248IL_25181.11
249IL_09491.11
250IL_58454.11
251IL_88367.11
252IL_49976.11
253IL_57285.11
254IL_30354.11

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_99438.11
9IL_54576.11
10IL_59018.11
11IL_60643.11
12IL_78809.11
13IL_37990.11
14IL_96182.11cWH basepair with syn base

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_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
4IL_33484.13cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
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