Changes in PDB files used for clustering

Release 0.7 has 192 PDB files, release 0.8 has 192 PDB files, 192 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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 0.7 has 263 motif groups, release 0.8 has 263 motif groups, 263 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.

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_97217.2234
2IL_47174.220016S h34 ILa : Part of larger motif
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.231Triple sheared
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_93424.222tSH-inserted-tHW
11IL_65553.221Kink-turn
12IL_32390.22116S h19 IL and 23S H41 IL
13IL_73276.120C-loop
14IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.21716S h21 S8 binding site
16IL_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
17IL_85647.216Sarcin-ricin parent motif with 15 Nts
18IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19IL_31555.21516S decoding site
20IL_94430.21416S h32-h33-h34 3WJ
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_40090.21116S h34 ILa : Part of larger motif
23IL_27618.21123S H73 ILa : Part of larger Motif
24IL_46648.11123S H91 IL | Single-Base Intercalation Site
25IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_58291.29Recurrent Sub-motif found in junctions
28IL_47444.29SRP Loop E-like motif
29IL_92114.29GAAA loop receptor "platform" motif
30IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_90459.28cWW AG or UU
33IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_73000.27cHS-cWS
35IL_86357.27LSU Helix 61 IL2
36IL_72158.26LSU Helix 62 (H62) IL
37IL_70237.36
38IL_53635.26LSU Helix 32 (H32) IL
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_24022.26
41IL_25230.26Bacterial 5S rRNA Loop E
42IL_89088.1616S h19 IL and 23S H41 IL
43IL_10007.16Single sheared with bulged bases
44IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45IL_08926.1623S H91 IL
46IL_97057.26
47IL_80179.25
48IL_01239.15
49IL_92484.15
50IL_82188.15LSU H68 IL from H.m.
51IL_07911.15
52IL_78732.35Double S-turn motif
53IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
54IL_02359.25
55IL_45262.25
56IL_40387.25
57IL_77263.15Kink-turn from U4
58IL_79083.25
59IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
60IL_98591.24
61IL_64184.24
62IL_22732.14tSH-inserted-tHS
63IL_39526.24
64IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
65IL_21333.14tSH-tHW-bulge
66IL_98556.14
67IL_38807.24
68IL_28572.1416S h18 kink-turn like motif
69IL_31066.24SSU Helix 44 (h44) extension
70IL_45808.13
71IL_52173.13
72IL_75447.13
73IL_98421.13
74IL_58586.23
75IL_82563.13Thi-box riboswitch T-loop
76IL_16252.2323S H91 IL
77IL_15840.13
78IL_71565.13
79IL_79955.23SSU Helix (23) h23 IL1
80IL_95150.23
81IL_80494.23LSU H58 IL2 H.m.
82IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
83IL_30840.13
84IL_37053.13Kink-turn from 23S H58
85IL_34628.23Kink-turn
86IL_62499.23
87IL_34156.23cWW AG or UU
88IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
89IL_43946.13
90IL_09348.23
91IL_53774.13Single sheared with bulged bases
92IL_34363.13Kink-turn from 23S H42
93IL_23262.33
94IL_31707.12Vitamin B12 aptamer
95IL_98566.12
96IL_87173.12
97IL_25174.12
98IL_37197.12
99IL_81441.12
100IL_92459.12
101IL_94744.12Sarcin-ricin motif with extra cWW GA pair
102IL_55287.12
103IL_45794.12
104IL_99575.12
105IL_48285.12Leadzyme Motif
106IL_80093.12
107IL_82831.22Kink-turn from 16S H23
108IL_00998.12
109IL_91026.12
110IL_50521.12
111IL_09882.12
112IL_12269.12
113IL_46435.12
114IL_23414.12
115IL_43933.12
116IL_16330.12
117IL_40892.12
118IL_87548.12
119IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
120IL_52940.12
121IL_90057.12
122IL_12211.12
123IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
124IL_21495.12
125IL_28942.12
126IL_65137.12Kink-turn like motif in Group I Intron
127IL_78674.12tHS tHH bulge with S-turn
128IL_41397.22LSU Helix 96 (H96) IL2
129IL_74876.12
130IL_14023.12
131IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
132IL_97833.12
133IL_16166.12
134IL_74291.12
135IL_01054.12
136IL_37406.12
137IL_12068.12
138IL_76095.32Motif from Hairpin Ribozyme
139IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
140IL_70280.12Double sheared with wobble cWW.
141IL_25082.11
142IL_98924.11
143IL_25181.11
144IL_82601.11Tandem cWW water-inserted CU pairs
145IL_41139.11
146IL_92280.11
147IL_91379.11
148IL_11302.11
149IL_89794.11
150IL_07675.11tHS tHH bulge with S-turn
151IL_25739.11M-Box Riboswitch
152IL_37715.11
153IL_22579.11
154IL_41849.11
155IL_75328.11
156IL_95939.11
157IL_24143.11Yeast 18S
158IL_71685.11Sarcin-like with an intercalated basepair
159IL_90880.11
160IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
161IL_96260.11
162IL_02835.11
163IL_68827.11Reverse Kink-Turn
164IL_22858.11
165IL_66744.11SSU Helix 21 (h21) IL2 E.coli
166IL_53988.11
167IL_20775.11tSH-inserted
168IL_61730.11
169IL_53423.11
170IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
171IL_23639.11tWH-tHS-L-cWW
172IL_17603.11
173IL_15205.11
174IL_91089.11
175IL_85805.11
176IL_03110.11
177IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
178IL_05462.11
179IL_06808.11Double sheared (tSH-tSH) one bulged base.
180IL_65788.11
181IL_55934.11kink-turn-like
182IL_27243.11
183IL_78809.11
184IL_13682.11
185IL_67735.11
186IL_76486.11Sarcin-ricin motif with syn G
187IL_37990.11
188IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
189IL_47457.11
190IL_23448.11
191IL_83250.1116S h40 3WJ T.th.
192IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
193IL_43316.11
194IL_83920.11
195IL_88403.11
196IL_80652.11
197IL_32080.11
198IL_61723.11
199IL_54576.11
200IL_97842.11
201IL_56513.11
202IL_30390.11
203IL_60643.11
204IL_57977.11
205IL_39324.11
206IL_41791.11
207IL_86059.11
208IL_12507.11
209IL_06468.1116S h40 3WJ E.c.
210IL_52958.11
211IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
212IL_97073.11
213IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
214IL_29949.11
215IL_75415.11Pseudo-knot forming internal loop
216IL_06306.11
217IL_37347.11
218IL_46306.11
219IL_91904.11
220IL_21421.11
221IL_85510.11
222IL_63952.11
223IL_52752.11
224IL_13942.11
225IL_80505.11
226IL_47687.11
227IL_62352.11
228IL_02690.11
229IL_11869.11
230IL_41009.11
231IL_81398.11
232IL_05221.11
233IL_26971.11
234IL_07375.11
235IL_58454.11
236IL_88367.11
237IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
238IL_82650.11
239IL_31006.11tSH-tHW-L-bif-cWW
240IL_52509.11
241IL_12486.11
242IL_12233.11
243IL_77014.11
244IL_03741.11
245IL_82113.11
246IL_53323.11
247IL_59529.11
248IL_02957.11
249IL_18755.11
250IL_40527.11Kink-turn
251IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
252IL_40845.11
253IL_88865.11
254IL_76263.11
255IL_25307.11
256IL_26868.11
257IL_55649.11
258IL_54450.11
259IL_31241.11
260IL_26241.11
261IL_71942.11
262IL_91078.11
263IL_56779.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription