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_65553.522Kink-turn
11IL_93424.322tSH-inserted-tHW
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_85647.316Sarcin-ricin parent motif with 15 Nts
16IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_94430.41516S h32-h33-h34 3WJ
19IL_31555.315Tandem sheared with inserted, unpaired purine.
20IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
22IL_46648.21123S H91 IL | Single-Base Intercalation Site
23IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24IL_40090.31116S h34 ILa : Part of larger motif
25IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_58291.39Recurrent Sub-motif found in junctions
27IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_90459.39cWW AG or UU
29IL_92114.39GAAA loop receptor "platform" motif
30IL_47444.39SRP Loop E-like motif
31IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
32IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33IL_73000.27cHS-cWS
34IL_70237.36
35IL_90133.26
36IL_25230.36Bacterial 5S rRNA Loop E
37IL_53635.36LSU Helix 32 (H32) IL
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
40IL_54420.16
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_72158.36LSU Helix 62 (H62) IL
43IL_97057.36
44IL_78732.35Double S-turn motif
45IL_86357.35LSU Helix 61 IL2
46IL_16207.15Single sheared with bulged bases
47IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48IL_79083.35
49IL_08926.2523S H91 IL
50IL_25300.1516S h19 IL and 23S H41 IL
51IL_82188.15LSU H68 IL from H.m.
52IL_45262.35
53IL_77263.15Kink-turn from U4
54IL_92484.15
55IL_02359.35
56IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
57IL_22732.14tSH-inserted-tHS
58IL_31066.24SSU Helix 44 (h44) extension
59IL_34363.24Kink-turn from 23S H42
60IL_16166.3423S H91 IL
61IL_28572.1416S h18 kink-turn like motif
62IL_38807.34
63IL_08559.14LSU Helix 89 (H89) IL2
64IL_39526.44
65IL_01080.14
66IL_21333.24tSH-tHW-bulge
67IL_42251.14
68IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
69IL_98591.34
70IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
71IL_30840.13
72IL_34156.63cWW AG or UU
73IL_48918.23Kink-turn variant
74IL_62499.63
75IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
76IL_34628.23Kink-turn
77IL_43946.13
78IL_58586.23
79IL_75447.13
80IL_05723.13
81IL_56077.13
82IL_92267.1323S H73 ILa : Part of larger Motif
83IL_10647.13tHS tHH bulge with S-turn
84IL_37053.13Kink-turn from 23S H58
85IL_52173.13
86IL_79955.23SSU Helix (23) h23 IL1
87IL_95150.33
88IL_82563.13Thi-box riboswitch T-loop
89IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
90IL_98421.33SSU Helix 12 (h12) IL
91IL_80348.1323S H91 IL
92IL_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.
93IL_80494.23LSU H58 IL2 H.m.
94IL_12211.12
95IL_21495.12
96IL_27892.12
97IL_46435.12
98IL_55287.12
99IL_69536.12LSU Helix 96 (H96) IL2
100IL_90057.12
101IL_09587.12
102IL_15840.22Triple Sheared with unpaired, inserted A
103IL_19898.12
104IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
105IL_07300.12
106IL_09882.12
107IL_23262.42
108IL_40892.12
109IL_49550.12tHS tHH bulge with S-turn
110IL_70280.12Double sheared with wobble cWW.
111IL_87548.12
112IL_94744.12Sarcin-ricin motif with extra cWW GA pair
113IL_09901.12tHS tHH bulge with S-turn
114IL_23414.12
115IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
116IL_50521.12
117IL_65137.12Kink-turn like motif in Group I Intron
118IL_76095.32Motif from Hairpin Ribozyme
119IL_97833.12
120IL_00998.12
121IL_16252.3223S H91 IL
122IL_28942.12
123IL_31707.12Vitamin B12 aptamer
124IL_88180.12cWW-bulge-cWW
125IL_01054.12
126IL_16330.12
127IL_24358.12
128IL_37197.12
129IL_77076.12
130IL_80093.12
131IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
132IL_11751.12
133IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
134IL_33925.12
135IL_45794.12
136IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
137IL_91273.12
138IL_98566.12
139IL_33964.12
140IL_37406.12
141IL_52940.12
142IL_02690.11
143IL_04550.11tHS tHH bulge with S-turn
144IL_06808.11Double sheared (tSH-tSH) one bulged base.
145IL_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.
146IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
147IL_25082.11
148IL_37715.11
149IL_40527.11Kink-turn
150IL_52958.11
151IL_80505.11
152IL_83250.1116S h40 3WJ T.th.
153IL_97073.11
154IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
155IL_05221.11
156IL_06847.11Group II Intron IL
157IL_12486.11
158IL_25181.11
159IL_28468.11Single sheared with bulged bases
160IL_37990.11
161IL_40845.11
162IL_43316.11
163IL_53323.11
164IL_55649.11
165IL_58454.11
166IL_63952.11
167IL_75415.11Pseudo-knot forming internal loop
168IL_80652.11
169IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
170IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
171IL_98924.11
172IL_02835.11
173IL_05462.11
174IL_12507.11
175IL_20775.11tSH-inserted
176IL_31290.11
177IL_46721.11
178IL_64589.11
179IL_78809.11
180IL_81398.11
181IL_83856.11
182IL_02957.11
183IL_21221.11SSU Helix 12 (h12) IL
184IL_28644.11
185IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
186IL_41139.11
187IL_53988.11
188IL_59529.11
189IL_82113.11
190IL_83920.11
191IL_91044.11
192IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
193IL_03110.11
194IL_06306.11
195IL_13434.11
196IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
197IL_23639.11tWH-tHS-L-cWW
198IL_39324.11
199IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
200IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
201IL_71685.11Sarcin-like with an intercalated basepair
202IL_76486.11Sarcin-ricin motif with syn G
203IL_85510.11
204IL_91078.11
205IL_92280.11
206IL_97842.11
207IL_03282.11
208IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
209IL_11302.11
210IL_13682.11
211IL_25307.11
212IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
213IL_47687.11
214IL_52509.11
215IL_54450.11
216IL_56513.11
217IL_60643.11
218IL_65788.11
219IL_71942.11
220IL_88367.11
221IL_91089.11
222IL_03741.11
223IL_06468.1116S h40 3WJ E.c.
224IL_26868.11
225IL_30067.11
226IL_37347.11
227IL_41791.11
228IL_47732.11
229IL_52610.11
230IL_54576.11
231IL_60649.11Kink-turn
232IL_66744.11SSU Helix 21 (h21) IL2 E.coli
233IL_82601.11Tandem cWW water-inserted CU pairs
234IL_85805.11
235IL_95774.11tHS tHH bulge with S-turn
236IL_03931.1116S h19 IL and 23S H41 IL
237IL_06471.11
238IL_09491.11
239IL_11778.11
240IL_15205.11
241IL_17603.11
242IL_21421.11
243IL_26971.11
244IL_30354.11
245IL_46306.11
246IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
247IL_57977.11
248IL_61730.11
249IL_67735.11
250IL_77296.11
251IL_82650.11
252IL_86059.11
253IL_89794.11
254IL_91904.11

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