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_93424.322tSH-inserted-tHW
11IL_65553.522Kink-turn
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_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
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_40090.31116S h34 ILa : Part of larger motif
22IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
23IL_46648.21123S H91 IL | Single-Base Intercalation Site
24IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
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_73000.27cHS-cWS
32IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35IL_72158.36LSU Helix 62 (H62) IL
36IL_97057.36
37IL_70237.36
38IL_90133.26
39IL_25230.36Bacterial 5S rRNA Loop E
40IL_53635.36LSU Helix 32 (H32) IL
41IL_13069.36LSU 3WJ H32-H33-H35A
42IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43IL_54420.16
44IL_77263.15Kink-turn from U4
45IL_92484.15
46IL_02359.35
47IL_78732.35Double S-turn motif
48IL_86357.35LSU Helix 61 IL2
49IL_16207.15Single sheared with bulged bases
50IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
51IL_79083.35
52IL_08926.2523S H91 IL
53IL_25300.1516S h19 IL and 23S H41 IL
54IL_82188.15LSU H68 IL from H.m.
55IL_45262.35
56IL_01080.14
57IL_21333.24tSH-tHW-bulge
58IL_42251.14
59IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_98591.34
61IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62IL_22732.14tSH-inserted-tHS
63IL_31066.24SSU Helix 44 (h44) extension
64IL_34363.24Kink-turn from 23S H42
65IL_16166.3423S H91 IL
66IL_28572.1416S h18 kink-turn like motif
67IL_38807.34
68IL_08559.14LSU Helix 89 (H89) IL2
69IL_39526.44
70IL_80348.1323S H91 IL
71IL_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.
72IL_80494.23LSU H58 IL2 H.m.
73IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
74IL_30840.13
75IL_34156.63cWW AG or UU
76IL_48918.23Kink-turn variant
77IL_62499.63
78IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
79IL_34628.23Kink-turn
80IL_43946.13
81IL_58586.23
82IL_75447.13
83IL_05723.13
84IL_56077.13
85IL_92267.1323S H73 ILa : Part of larger Motif
86IL_10647.13tHS tHH bulge with S-turn
87IL_37053.13Kink-turn from 23S H58
88IL_52173.13
89IL_79955.23SSU Helix (23) h23 IL1
90IL_95150.33
91IL_82563.13Thi-box riboswitch T-loop
92IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
93IL_98421.33SSU Helix 12 (h12) IL
94IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
95IL_11751.12
96IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
97IL_33925.12
98IL_45794.12
99IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
100IL_91273.12
101IL_98566.12
102IL_33964.12
103IL_37406.12
104IL_52940.12
105IL_12211.12
106IL_21495.12
107IL_27892.12
108IL_46435.12
109IL_55287.12
110IL_69536.12LSU Helix 96 (H96) IL2
111IL_90057.12
112IL_09587.12
113IL_15840.22Triple Sheared with unpaired, inserted A
114IL_19898.12
115IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
116IL_07300.12
117IL_09882.12
118IL_23262.42
119IL_40892.12
120IL_49550.12tHS tHH bulge with S-turn
121IL_70280.12Double sheared with wobble cWW.
122IL_87548.12
123IL_94744.12Sarcin-ricin motif with extra cWW GA pair
124IL_09901.12tHS tHH bulge with S-turn
125IL_23414.12
126IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
127IL_50521.12
128IL_65137.12Kink-turn like motif in Group I Intron
129IL_76095.32Motif from Hairpin Ribozyme
130IL_97833.12
131IL_00998.12
132IL_16252.3223S H91 IL
133IL_28942.12
134IL_31707.12Vitamin B12 aptamer
135IL_88180.12cWW-bulge-cWW
136IL_01054.12
137IL_16330.12
138IL_24358.12
139IL_37197.12
140IL_77076.12
141IL_80093.12
142IL_03741.11
143IL_06468.1116S h40 3WJ E.c.
144IL_26868.11
145IL_30067.11
146IL_37347.11
147IL_41791.11
148IL_47732.11
149IL_52610.11
150IL_54576.11
151IL_60649.11Kink-turn
152IL_66744.11SSU Helix 21 (h21) IL2 E.coli
153IL_82601.11Tandem cWW water-inserted CU pairs
154IL_85805.11
155IL_95774.11tHS tHH bulge with S-turn
156IL_03931.1116S h19 IL and 23S H41 IL
157IL_06471.11
158IL_09491.11
159IL_11778.11
160IL_15205.11
161IL_17603.11
162IL_21421.11
163IL_26971.11
164IL_30354.11
165IL_46306.11
166IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
167IL_57977.11
168IL_61730.11
169IL_67735.11
170IL_77296.11
171IL_82650.11
172IL_86059.11
173IL_89794.11
174IL_91904.11
175IL_02690.11
176IL_04550.11tHS tHH bulge with S-turn
177IL_06808.11Double sheared (tSH-tSH) one bulged base.
178IL_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.
179IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
180IL_25082.11
181IL_37715.11
182IL_40527.11Kink-turn
183IL_52958.11
184IL_80505.11
185IL_83250.1116S h40 3WJ T.th.
186IL_97073.11
187IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
188IL_05221.11
189IL_06847.11Group II Intron IL
190IL_12486.11
191IL_25181.11
192IL_28468.11Single sheared with bulged bases
193IL_37990.11
194IL_40845.11
195IL_43316.11
196IL_53323.11
197IL_55649.11
198IL_58454.11
199IL_63952.11
200IL_75415.11Pseudo-knot forming internal loop
201IL_80652.11
202IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
203IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
204IL_98924.11
205IL_02835.11
206IL_05462.11
207IL_12507.11
208IL_20775.11tSH-inserted
209IL_31290.11
210IL_46721.11
211IL_64589.11
212IL_78809.11
213IL_81398.11
214IL_83856.11
215IL_02957.11
216IL_21221.11SSU Helix 12 (h12) IL
217IL_28644.11
218IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
219IL_41139.11
220IL_53988.11
221IL_59529.11
222IL_82113.11
223IL_83920.11
224IL_91044.11
225IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
226IL_03110.11
227IL_06306.11
228IL_13434.11
229IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
230IL_23639.11tWH-tHS-L-cWW
231IL_39324.11
232IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
233IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
234IL_71685.11Sarcin-like with an intercalated basepair
235IL_76486.11Sarcin-ricin motif with syn G
236IL_85510.11
237IL_91078.11
238IL_92280.11
239IL_97842.11
240IL_03282.11
241IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
242IL_11302.11
243IL_13682.11
244IL_25307.11
245IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
246IL_47687.11
247IL_52509.11
248IL_54450.11
249IL_56513.11
250IL_60643.11
251IL_65788.11
252IL_71942.11
253IL_88367.11
254IL_91089.11

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