Changes in PDB files used for clustering

Release 1.3 has 200 PDB files, release 1.4 has 201 PDB files, 200 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.4: 4KYY.

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 1.3 has 271 motif groups, release 1.4 has 271 motif groups, 269 of them are identical.

2 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.

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_39199.354Hoogsteen-edge Platform, Single bulged base
3IL_41766.349Tandem cWW pairs (Not AU or GC)
4IL_56465.346Single, unpaired intercalated base, consensus A
5IL_44540.343Sugar-edge, 1-base platform, consensus tHS
6IL_87904.431Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_06390.326cWH basepair with syn base
8IL_13959.324Double Sheared (tSH-tHS)
9IL_65553.522Kink-turn
10IL_93424.322tSH-inserted-tHW
11IL_73276.321C-loop
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_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
23IL_46648.21123S H91 IL | Single-Base Intercalation Site
24IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
25IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
26IL_92114.39GAAA loop receptor "platform" motif
27IL_58291.39Recurrent Sub-motif found in junctions
28IL_90459.39cWW AG or UU
29IL_47444.39SRP Loop E-like motif
30IL_73000.27cHS-cWS
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_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
34IL_97057.36
35IL_53635.36LSU Helix 32 (H32) IL
36IL_90133.26
37IL_72158.36LSU Helix 62 (H62) IL
38IL_13069.36LSU 3WJ H32-H33-H35A
39IL_54420.16
40IL_70237.36
41IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_25230.36Bacterial 5S rRNA Loop E
43IL_77263.15Kink-turn from U4
44IL_86357.35LSU Helix 61 IL2
45IL_16207.15Single sheared with bulged bases
46IL_08926.2523S H91 IL
47IL_02359.35
48IL_92484.15
49IL_78732.35Double S-turn motif
50IL_82188.15LSU H68 IL from H.m.
51IL_25300.1516S h19 IL and 23S H41 IL
52IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
53IL_45262.35
54IL_79083.35
55IL_28572.1416S h18 kink-turn like motif
56IL_31066.24SSU Helix 44 (h44) extension
57IL_21333.24tSH-tHW-bulge
58IL_34363.24Kink-turn from 23S H42
59IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_01080.14
61IL_16166.3423S H91 IL
62IL_08559.14LSU Helix 89 (H89) IL2
63IL_22732.14tSH-inserted-tHS
64IL_98591.34
65IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
66IL_39526.44
67IL_94403.14LSU H77
68IL_42251.14
69IL_38807.34
70IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
71IL_43946.13
72IL_80348.1323S H91 IL
73IL_52173.13
74IL_75447.13
75IL_48918.23Kink-turn variant
76IL_98421.33SSU Helix 12 (h12) IL
77IL_82563.13Thi-box riboswitch T-loop
78IL_10647.13tHS tHH bulge with S-turn
79IL_95150.33
80IL_58586.23
81IL_30840.13
82IL_05723.13
83IL_79955.23SSU Helix (23) h23 IL1
84IL_80494.23LSU H58 IL2 H.m.
85IL_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.
86IL_34628.23Kink-turn
87IL_62499.63
88IL_71565.33
89IL_37053.13Kink-turn from 23S H58
90IL_92267.1323S H73 ILa : Part of larger Motif
91IL_56077.13
92IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
93IL_34156.63cWW AG or UU
94IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
95IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
96IL_55287.12
97IL_31707.12Vitamin B12 aptamer
98IL_97833.12
99IL_98566.12
100IL_00998.12
101IL_16252.3223S H91 IL
102IL_94744.12Sarcin-ricin motif with extra cWW GA pair
103IL_76095.32Motif from Hairpin Ribozyme
104IL_91273.12
105IL_27892.12
106IL_23414.12
107IL_37197.12
108IL_09587.12
109IL_07300.12
110IL_45794.12
111IL_33964.12
112IL_50521.12
113IL_09882.12
114IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
115IL_80093.12
116IL_46435.12
117IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
118IL_09901.12tHS tHH bulge with S-turn
119IL_24358.12
120IL_16330.12
121IL_87548.12
122IL_52940.12
123IL_21495.12
124IL_37406.12
125IL_69536.12LSU Helix 96 (H96) IL2
126IL_28942.12
127IL_40892.12
128IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
129IL_65137.12Kink-turn like motif in Group I Intron
130IL_77076.12
131IL_12211.12
132IL_01054.12
133IL_15840.22Triple Sheared with unpaired, inserted A
134IL_23262.42
135IL_49550.12tHS tHH bulge with S-turn
136IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
137IL_11751.12
138IL_19898.12
139IL_90057.12
140IL_33925.12
141IL_70280.12Double sheared with wobble cWW.
142IL_88180.12cWW-bulge-cWW
143IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
144IL_25307.11
145IL_11302.11
146IL_53988.11
147IL_28644.11
148IL_11778.11
149IL_37715.11
150IL_54450.11
151IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
152IL_25082.11
153IL_98924.11
154IL_59529.11
155IL_02957.11
156IL_28468.11Single sheared with bulged bases
157IL_88367.11
158IL_60649.11Kink-turn
159IL_47732.11
160IL_40845.11
161IL_76263.11
162IL_04550.11tHS tHH bulge with S-turn
163IL_66744.11SSU Helix 21 (h21) IL2 E.coli
164IL_05462.11
165IL_20775.11tSH-inserted
166IL_13682.11
167IL_31290.11
168IL_13434.11
169IL_71685.11Sarcin-like with an intercalated basepair
170IL_25181.11
171IL_58454.11
172IL_40527.11Kink-turn
173IL_77296.11
174IL_30354.11
175IL_68827.11Reverse Kink-Turn
176IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
177IL_06808.11Double sheared (tSH-tSH) one bulged base.
178IL_61730.11
179IL_67735.11
180IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
181IL_23639.11tWH-tHS-L-cWW
182IL_64589.11
183IL_41139.11
184IL_03282.11
185IL_46721.11
186IL_85805.11
187IL_92280.11
188IL_02835.11
189IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
190IL_83920.11
191IL_52958.11
192IL_80652.11
193IL_65788.11
194IL_78809.11
195IL_75415.11Pseudo-knot forming internal loop
196IL_76486.11Sarcin-ricin motif with syn G
197IL_37990.11
198IL_82601.11Tandem cWW water-inserted CU pairs
199IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
200IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
201IL_83250.1116S h40 3WJ T.th.
202IL_03110.11
203IL_06468.1116S h40 3WJ E.c.
204IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
205IL_97073.11
206IL_03931.1116S h19 IL and 23S H41 IL
207IL_54576.11
208IL_06306.11
209IL_97842.11
210IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
211IL_17603.11
212IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
213IL_91089.11
214IL_30067.11
215IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
216IL_41791.11
217IL_43316.11
218IL_12507.11
219IL_47687.11
220IL_21221.11SSU Helix 12 (h12) IL
221IL_03741.11
222IL_83856.11
223IL_37347.11
224IL_46306.11
225IL_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.
226IL_15205.11
227IL_60643.11
228IL_52610.11
229IL_63952.11
230IL_57977.11
231IL_39324.11
232IL_80505.11
233IL_55649.11
234IL_52509.11
235IL_02690.11
236IL_91078.11
237IL_81398.11
238IL_05221.11
239IL_06471.11
240IL_91904.11
241IL_56513.11
242IL_91044.11
243IL_87394.11
244IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
245IL_86059.11
246IL_82650.11
247IL_26868.11
248IL_89794.11
249IL_95774.11tHS tHH bulge with S-turn
250IL_12486.11
251IL_71942.11
252IL_82113.11
253IL_53323.11
254IL_26971.11
255IL_09491.11
256IL_21421.11
257IL_85510.11
258IL_06847.11Group II Intron IL
259IL_42891.11

Updated motif groups

#Motif idInstancesDescription
1IL_47174.7203cWW AG or water inserted cWW Y-Y.
2IL_40090.41216S h34 ILa : Part of larger motif

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription