Changes in PDB files used for clustering

Release 1.1 has 200 PDB files, release 1.2 has 201 PDB files, 200 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_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_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_40090.31116S h34 ILa : Part of larger motif
23IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
24IL_46648.21123S H91 IL | Single-Base Intercalation Site
25IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_92114.39GAAA loop receptor "platform" motif
28IL_58291.39Recurrent Sub-motif found in junctions
29IL_90459.39cWW AG or UU
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_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
35IL_97057.36
36IL_53635.36LSU Helix 32 (H32) IL
37IL_90133.26
38IL_72158.36LSU Helix 62 (H62) IL
39IL_13069.36LSU 3WJ H32-H33-H35A
40IL_70237.36
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_54420.16
43IL_25230.36Bacterial 5S rRNA Loop E
44IL_45262.35
45IL_86357.35LSU Helix 61 IL2
46IL_16207.15Single sheared with bulged bases
47IL_77263.15Kink-turn from U4
48IL_08926.2523S H91 IL
49IL_79083.35
50IL_92484.15
51IL_82188.15LSU H68 IL from H.m.
52IL_78732.35Double S-turn motif
53IL_02359.35
54IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
55IL_25300.1516S h19 IL and 23S H41 IL
56IL_42251.14
57IL_38807.34
58IL_28572.1416S h18 kink-turn like motif
59IL_21333.24tSH-tHW-bulge
60IL_16166.3423S H91 IL
61IL_34363.24Kink-turn from 23S H42
62IL_31066.24SSU Helix 44 (h44) extension
63IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
64IL_01080.14
65IL_98591.34
66IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67IL_22732.14tSH-inserted-tHS
68IL_08559.14LSU Helix 89 (H89) IL2
69IL_39526.44
70IL_62499.63
71IL_34156.63cWW AG or UU
72IL_10647.13tHS tHH bulge with S-turn
73IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
74IL_43946.13
75IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
76IL_56077.13
77IL_34628.23Kink-turn
78IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
79IL_80348.1323S H91 IL
80IL_52173.13
81IL_75447.13
82IL_98421.33SSU Helix 12 (h12) IL
83IL_58586.23
84IL_82563.13Thi-box riboswitch T-loop
85IL_95150.33
86IL_05723.13
87IL_79955.23SSU Helix (23) h23 IL1
88IL_80494.23LSU H58 IL2 H.m.
89IL_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.
90IL_30840.13
91IL_37053.13Kink-turn from 23S H58
92IL_92267.1323S H73 ILa : Part of larger Motif
93IL_48918.23Kink-turn variant
94IL_11751.12
95IL_65137.12Kink-turn like motif in Group I Intron
96IL_19898.12
97IL_33925.12
98IL_01054.12
99IL_15840.22Triple Sheared with unpaired, inserted A
100IL_37406.12
101IL_69536.12LSU Helix 96 (H96) IL2
102IL_28942.12
103IL_23414.12
104IL_37197.12
105IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
106IL_23262.42
107IL_07300.12
108IL_45794.12
109IL_33964.12
110IL_97833.12
111IL_98566.12
112IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
113IL_70280.12Double sheared with wobble cWW.
114IL_24358.12
115IL_16330.12
116IL_31707.12Vitamin B12 aptamer
117IL_76095.32Motif from Hairpin Ribozyme
118IL_40892.12
119IL_91273.12
120IL_00998.12
121IL_16252.3223S H91 IL
122IL_94744.12Sarcin-ricin motif with extra cWW GA pair
123IL_49550.12tHS tHH bulge with S-turn
124IL_96446.12
125IL_50521.12
126IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
127IL_80093.12
128IL_46435.12
129IL_09587.12
130IL_27892.12
131IL_88180.12cWW-bulge-cWW
132IL_87548.12
133IL_09882.12
134IL_77076.12
135IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
136IL_55287.12
137IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
138IL_52940.12
139IL_90057.12
140IL_12211.12
141IL_21495.12
142IL_09901.12tHS tHH bulge with S-turn
143IL_86059.11
144IL_82650.11
145IL_31006.11tSH-tHW-L-bif-cWW
146IL_21221.11SSU Helix 12 (h12) IL
147IL_54576.11
148IL_67735.11
149IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
150IL_23639.11tWH-tHS-L-cWW
151IL_64589.11
152IL_41139.11
153IL_77296.11
154IL_87394.11
155IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
156IL_25307.11
157IL_26868.11
158IL_55649.11
159IL_52509.11
160IL_02690.11
161IL_75415.11Pseudo-knot forming internal loop
162IL_76486.11Sarcin-ricin motif with syn G
163IL_37990.11
164IL_82601.11Tandem cWW water-inserted CU pairs
165IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
166IL_03282.11
167IL_42891.11
168IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
169IL_40845.11
170IL_88865.11
171IL_76263.11
172IL_91379.11
173IL_11302.11
174IL_89794.11
175IL_95774.11tHS tHH bulge with S-turn
176IL_12486.11
177IL_06306.11
178IL_97842.11
179IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
180IL_17603.11
181IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
182IL_91089.11
183IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
184IL_47732.11
185IL_68827.11Reverse Kink-Turn
186IL_04550.11tHS tHH bulge with S-turn
187IL_66744.11SSU Helix 21 (h21) IL2 E.coli
188IL_53988.11
189IL_28644.11
190IL_11778.11
191IL_37715.11
192IL_54450.11
193IL_77014.11
194IL_03741.11
195IL_83856.11
196IL_37347.11
197IL_46306.11
198IL_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.
199IL_15205.11
200IL_23448.11
201IL_57285.11
202IL_30354.11
203IL_92280.11
204IL_02835.11
205IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
206IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
207IL_05462.11
208IL_20775.11tSH-inserted
209IL_71942.11
210IL_91078.11
211IL_81398.11
212IL_05221.11
213IL_06471.11
214IL_91904.11
215IL_56513.11
216IL_60643.11
217IL_46721.11
218IL_85805.11
219IL_03110.11
220IL_83920.11
221IL_06808.11Double sheared (tSH-tSH) one bulged base.
222IL_27243.11
223IL_75328.11
224IL_82113.11
225IL_53323.11
226IL_26971.11
227IL_09491.11
228IL_21421.11
229IL_85510.11
230IL_91044.11
231IL_27668.11
232IL_83250.1116S h40 3WJ T.th.
233IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
234IL_41791.11
235IL_43316.11
236IL_12507.11
237IL_06468.1116S h40 3WJ E.c.
238IL_52958.11
239IL_80652.11
240IL_65788.11
241IL_61730.11
242IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
243IL_25082.11
244IL_98924.11
245IL_59529.11
246IL_02957.11
247IL_28468.11Single sheared with bulged bases
248IL_88367.11
249IL_06847.11Group II Intron IL
250IL_30067.11
251IL_63952.11
252IL_57977.11
253IL_39324.11
254IL_80505.11
255IL_47687.11
256IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
257IL_97073.11
258IL_03931.1116S h19 IL and 23S H41 IL
259IL_78809.11
260IL_13682.11
261IL_31290.11
262IL_13434.11
263IL_71685.11Sarcin-like with an intercalated basepair
264IL_25181.11
265IL_58454.11
266IL_40527.11Kink-turn
267IL_60649.11Kink-turn
268IL_52610.11

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