Changes in PDB files used for clustering

Release 0.8 has 192 PDB files, release 0.9 has 196 PDB files, 192 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 0.9: 4FNJ, 4FRG, 4GMA, 4GXY.

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 0.8 has 263 motif groups, release 0.9 has 264 motif groups, 224 of them are identical.

15 motif groups were updated, 24 groups are present only in release 0.8, 25 groups are only in release 0.9.

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_39199.255Hoogsteen-edge Platform, Single bulged base
2IL_41766.249Tandem cWW pairs (Not AU or GC)
3IL_56465.245Single, unpaired intercalated base, consensus A
4IL_44540.243Sugar-edge, 1-base platform, consensus tHS
5IL_87904.231Triple sheared
6IL_06390.125cWH basepair with syn base
7IL_13959.224Double Sheared (tSH-tHS)
8IL_93424.222tSH-inserted-tHW
9IL_32390.22116S h19 IL and 23S H41 IL
10IL_73276.120C-loop
11IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
12IL_92027.21716S h21 S8 binding site
13IL_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
14IL_85647.216Sarcin-ricin parent motif with 15 Nts
15IL_31555.21516S decoding site
16IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_27618.21123S H73 ILa : Part of larger Motif
19IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
20IL_46648.11123S H91 IL | Single-Base Intercalation Site
21IL_40090.21116S h34 ILa : Part of larger motif
22IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_47444.29SRP Loop E-like motif
24IL_92114.29GAAA loop receptor "platform" motif
25IL_58291.29Recurrent Sub-motif found in junctions
26IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28IL_90459.28cWW AG or UU
29IL_73000.27cHS-cWS
30IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31IL_86357.27LSU Helix 61 IL2
32IL_70237.36
33IL_97057.26
34IL_72158.26LSU Helix 62 (H62) IL
35IL_25230.26Bacterial 5S rRNA Loop E
36IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
37IL_53635.26LSU Helix 32 (H32) IL
38IL_89088.1616S h19 IL and 23S H41 IL
39IL_13069.26LSU 3WJ H32-H33-H35A
40IL_24022.26
41IL_10007.16Single sheared with bulged bases
42IL_08926.1623S H91 IL
43IL_01239.15
44IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
45IL_82188.15LSU H68 IL from H.m.
46IL_92484.15
47IL_02359.25
48IL_77263.15Kink-turn from U4
49IL_80179.25
50IL_78732.35Double S-turn motif
51IL_45262.25
52IL_79083.25
53IL_22732.14tSH-inserted-tHS
54IL_98591.24
55IL_28572.1416S h18 kink-turn like motif
56IL_21333.14tSH-tHW-bulge
57IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
58IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
59IL_31066.24SSU Helix 44 (h44) extension
60IL_38807.24
61IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
62IL_34363.13Kink-turn from 23S H42
63IL_23262.33
64IL_30840.13
65IL_53774.13Single sheared with bulged bases
66IL_71565.13
67IL_75447.13
68IL_80494.23LSU H58 IL2 H.m.
69IL_82563.13Thi-box riboswitch T-loop
70IL_37053.13Kink-turn from 23S H58
71IL_43946.13
72IL_79955.23SSU Helix (23) h23 IL1
73IL_16252.2323S H91 IL
74IL_52173.13
75IL_58586.23
76IL_34628.23Kink-turn
77IL_87548.12
78IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
79IL_81441.12
80IL_28942.12
81IL_74876.12
82IL_14023.12
83IL_37197.12
84IL_99575.12
85IL_98566.12
86IL_46435.12
87IL_45794.12
88IL_09882.12
89IL_12269.12
90IL_01054.12
91IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
92IL_90057.12
93IL_80093.12
94IL_00998.12
95IL_12068.12
96IL_25174.12
97IL_16330.12
98IL_40892.12
99IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
100IL_65137.12Kink-turn like motif in Group I Intron
101IL_12211.12
102IL_41397.22LSU Helix 96 (H96) IL2
103IL_70280.12Double sheared with wobble cWW.
104IL_94744.12Sarcin-ricin motif with extra cWW GA pair
105IL_55287.12
106IL_52940.12
107IL_97833.12
108IL_31707.12Vitamin B12 aptamer
109IL_76095.32Motif from Hairpin Ribozyme
110IL_82831.22Kink-turn from 16S H23
111IL_21495.12
112IL_37406.12
113IL_23414.12
114IL_50521.12
115IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
116IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
117IL_06468.1116S h40 3WJ E.c.
118IL_06808.11Double sheared (tSH-tSH) one bulged base.
119IL_11869.11
120IL_41009.11
121IL_25082.11
122IL_71685.11Sarcin-like with an intercalated basepair
123IL_56513.11
124IL_88367.11
125IL_63952.11
126IL_40845.11
127IL_57977.11
128IL_47687.11
129IL_89794.11
130IL_05462.11
131IL_02690.11
132IL_12233.11
133IL_77014.11
134IL_03741.11
135IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
136IL_23639.11tWH-tHS-L-cWW
137IL_21421.11
138IL_40527.11Kink-turn
139IL_02835.11
140IL_12507.11
141IL_53988.11
142IL_80652.11
143IL_97073.11
144IL_12486.11
145IL_31241.11
146IL_26241.11
147IL_71942.11
148IL_91078.11
149IL_76486.11Sarcin-ricin motif with syn G
150IL_37990.11
151IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
152IL_58454.11
153IL_41139.11
154IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
155IL_85805.11
156IL_43316.11
157IL_80505.11
158IL_26868.11
159IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
160IL_54450.11
161IL_41849.11
162IL_75328.11
163IL_53423.11
164IL_97842.11
165IL_18755.11
166IL_91089.11
167IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
168IL_83250.1116S h40 3WJ T.th.
169IL_86059.11
170IL_82650.11
171IL_11302.11
172IL_22579.11
173IL_61730.11
174IL_67735.11
175IL_37347.11
176IL_46306.11
177IL_91904.11
178IL_82601.11Tandem cWW water-inserted CU pairs
179IL_23448.11
180IL_88865.11
181IL_03110.11
182IL_41791.11
183IL_25307.11
184IL_66744.11SSU Helix 21 (h21) IL2 E.coli
185IL_52958.11
186IL_52509.11
187IL_37715.11
188IL_55934.11kink-turn-like
189IL_27243.11
190IL_78809.11
191IL_13682.11
192IL_06306.11
193IL_05221.11
194IL_26971.11
195IL_02957.11
196IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
197IL_60643.11
198IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
199IL_76263.11
200IL_91379.11
201IL_61723.11
202IL_54576.11
203IL_81398.11
204IL_53323.11
205IL_59529.11
206IL_90880.11
207IL_15205.11
208IL_92280.11
209IL_39324.11
210IL_68827.11Reverse Kink-Turn
211IL_83920.11
212IL_88403.11
213IL_31006.11tSH-tHW-L-bif-cWW
214IL_55649.11
215IL_20775.11tSH-inserted
216IL_65788.11
217IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
218IL_29949.11
219IL_75415.11Pseudo-knot forming internal loop
220IL_82113.11
221IL_98924.11
222IL_25181.11
223IL_17603.11
224IL_85510.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.3235
2IL_47174.320216S h34 ILa : Part of larger motif
3IL_65553.323Kink-turn
4IL_94430.31516S h32-h33-h34 3WJ
5IL_39526.34
6IL_40387.34
7IL_98556.24
8IL_16166.23
9IL_95150.33
10IL_98421.23SSU Helix 12 (h12) IL
11IL_62499.33
12IL_09348.33cWW-L-cWW-cWW
13IL_89028.23Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
14IL_34156.32cWW AG or UU
15IL_15840.22Triple Sheared with unpaired, inserted A

Removed motif groups

#Motif idInstancesDescription
1IL_07911.15
2IL_64184.24
3IL_45808.13
4IL_78674.12tHS tHH bulge with S-turn
5IL_87173.12
6IL_48285.12Leadzyme Motif
7IL_91026.12
8IL_92459.12
9IL_43933.12
10IL_74291.12
11IL_13942.11
12IL_47457.11
13IL_22858.11
14IL_24143.11Yeast 18S
15IL_52752.11
16IL_25739.11M-Box Riboswitch
17IL_56779.11
18IL_95939.11
19IL_30390.11
20IL_62352.11
21IL_96260.11
22IL_07375.11
23IL_32080.11
24IL_07675.11tHS tHH bulge with S-turn

Added motif groups

#Motif idInstancesDescription
1IL_54420.16
2IL_90133.15
3IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
4IL_36254.13
5IL_86826.13tHS tHH bulge with S-turn
6IL_07300.12
7IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
8IL_11751.12
9IL_91132.12
10IL_73816.12tHS tHH bulge with S-turn
11IL_37737.12
12IL_93782.12
13IL_80755.12
14IL_96446.12
15IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
16IL_61991.11
17IL_62017.11Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
18IL_27668.11
19IL_70550.11
20IL_76256.11
21IL_06471.11
22IL_83856.11
23IL_98688.11
24IL_06780.11
25IL_57285.11