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_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_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
20IL_31555.413Tandem sheared with inserted, unpaired purine.
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_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_97057.36
30IL_08926.3623S H91 IL
31IL_25230.36Bacterial 5S rRNA Loop E
32IL_53635.36LSU Helix 32 (H32) IL
33IL_90133.36
34IL_72158.36LSU Helix 62 (H62) IL
35IL_13069.36LSU 3WJ H32-H33-H35A
36IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37IL_77263.26Kink-turn from U4
38IL_25380.16LSU Helix 89 (H89) IL2
39IL_70237.36
40IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
41IL_25300.1516S h19 IL and 23S H41 IL
42IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
43IL_86357.35LSU Helix 61 IL2
44IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45IL_79083.35
46IL_02359.35
47IL_31663.1423S H73 ILa : Part of larger Motif
48IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
49IL_22732.14tSH-inserted-tHS
50IL_38807.34
51IL_45262.44
52IL_42251.14
53IL_34363.24Kink-turn from 23S H42
54IL_21333.24tSH-tHW-bulge
55IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
56IL_39980.14
57IL_98591.34
58IL_09530.14Double S-turn motif
59IL_28572.2416S h18 kink-turn like motif
60IL_31066.34SSU Helix 44 (h44) extension
61IL_82188.24LSU H68 IL from H.m.
62IL_39526.44
63IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
64IL_01080.14
65IL_98421.43SSU Helix 12 (h12) IL
66IL_37053.13Kink-turn from 23S H58
67IL_06180.13tHS tHH bulge with S-turn
68IL_06211.13
69IL_43946.13
70IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
71IL_30840.23
72IL_79955.23SSU Helix (23) h23 IL1
73IL_95150.43
74IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
75IL_16166.4323S H91 IL
76IL_75447.13
77IL_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.
78IL_34628.23Kink-turn
79IL_07300.23
80IL_62499.73
81IL_82563.13Thi-box riboswitch T-loop
82IL_87065.1323S H91 IL | Single-Base Intercalation Site
83IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
84IL_48918.23Kink-turn variant
85IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
86IL_52173.13
87IL_58586.23
88IL_05723.13
89IL_80348.1323S H91 IL
90IL_80494.23LSU H58 IL2 H.m.
91IL_09882.12
92IL_77076.12
93IL_01054.12
94IL_15840.22Triple Sheared with unpaired, inserted A
95IL_94744.12Sarcin-ricin motif with extra cWW GA pair
96IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
97IL_90057.12
98IL_96206.12
99IL_23262.42
100IL_69536.12LSU Helix 96 (H96) IL2
101IL_23414.12
102IL_50521.12
103IL_19898.12
104IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
105IL_46034.12
106IL_87548.12
107IL_52940.12
108IL_98566.12
109IL_30381.12tHS tHH bulge with S-turn
110IL_67887.12
111IL_21639.12
112IL_37197.12
113IL_96446.12
114IL_11751.12
115IL_65137.12Kink-turn like motif in Group I Intron
116IL_97833.12
117IL_00998.12
118IL_45794.12
119IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
120IL_76095.32Motif from Hairpin Ribozyme
121IL_46435.12
122IL_09587.12
123IL_16330.12
124IL_87507.12tHS tHH bulge with S-turn
125IL_80093.12
126IL_97509.12Double sheared with wobble cWW.
127IL_40892.12
128IL_33964.12
129IL_31707.12Vitamin B12 aptamer
130IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
131IL_12211.12
132IL_21495.12
133IL_37406.12
134IL_90735.12
135IL_50911.1116S h34 ILa : Part of larger motif
136IL_39324.11
137IL_06177.11cWW AG or UU
138IL_82650.11
139IL_31006.11tSH-tHW-L-bif-cWW
140IL_55649.11
141IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
142IL_13682.11
143IL_31224.1123S H91 IL
144IL_05221.11
145IL_26971.11
146IL_56513.11
147IL_15205.11
148IL_21077.11
149IL_03282.11
150IL_42891.11
151IL_85805.11
152IL_57977.11
153IL_86059.11
154IL_25307.11
155IL_26868.11
156IL_27243.11
157IL_25082.11
158IL_53323.11
159IL_59529.11
160IL_91904.11
161IL_21421.11
162IL_85510.11
163IL_49527.11
164IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
165IL_47732.11
166IL_83250.1116S h40 3WJ T.th.
167IL_76263.11
168IL_91379.11
169IL_11302.11
170IL_89794.11
171IL_28644.11
172IL_52509.11
173IL_61730.11
174IL_75415.11Pseudo-knot forming internal loop
175IL_88119.11
176IL_98924.11
177IL_25181.11
178IL_09491.11
179IL_58454.11
180IL_88367.11
181IL_49976.11
182IL_57285.11
183IL_30354.11
184IL_68827.11Reverse Kink-Turn
185IL_66744.11SSU Helix 21 (h21) IL2 E.coli
186IL_53988.11
187IL_71685.11Sarcin-like with an intercalated basepair
188IL_02957.11
189IL_18675.11cWW-bulge-cWW
190IL_40527.11Kink-turn
191IL_23448.11
192IL_46721.11
193IL_63952.11
194IL_88865.11
195IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
196IL_83920.11
197IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
198IL_11778.11
199IL_03741.11
200IL_06306.11
201IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
202IL_23639.11tWH-tHS-L-cWW
203IL_57364.11LSU Helix 89 (H89) IL2
204IL_41139.11
205IL_91044.11
206IL_27668.11
207IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
208IL_02835.11
209IL_06421.11Single sheared with bulged bases
210IL_20775.11tSH-inserted
211IL_77014.11
212IL_91078.11
213IL_83856.11
214IL_76486.11Sarcin-ricin motif with syn G
215IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
216IL_64589.11
217IL_54470.11tHS tHH bulge with S-turn
218IL_06847.11Group II Intron IL
219IL_30067.11
220IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
221IL_40845.11
222IL_92280.11
223IL_03110.11
224IL_43316.11
225IL_12507.11
226IL_06468.1116S h40 3WJ E.c.
227IL_52958.11
228IL_06808.11Double sheared (tSH-tSH) one bulged base.
229IL_71942.11
230IL_81398.11
231IL_97842.11
232IL_46306.11
233IL_82601.11Tandem cWW water-inserted CU pairs
234IL_91089.11
235IL_60649.11Kink-turn
236IL_52610.11
237IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
238IL_41791.11
239IL_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.
240IL_80505.11
241IL_69799.11
242IL_47687.11
243IL_80652.11
244IL_54450.11
245IL_75328.11
246IL_20530.11
247IL_37347.11
248IL_06471.11
249IL_68767.11
250IL_17603.11
251IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
252IL_87523.11
253IL_77296.11
254IL_87394.11

Updated motif groups

#Motif idInstancesDescription
1IL_65553.722Kink-turn
2IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
3IL_46648.41123S H91 IL | Single-Base Intercalation Site
4IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_71565.44
3IL_15768.14cWW AG or UU | cWH basepair with syn base
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_78809.11
9IL_37990.11
10IL_96182.11cWH basepair with syn base
11IL_99438.11
12IL_54576.11
13IL_59018.11
14IL_60643.11

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_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