Changes in PDB files used for clustering

Release 1.1 has 199 PDB files, release 1.9 has 209 PDB files, 197 of them are identical.

2 equivalence classes changed representatives: 2XZM4BPP, 3NPB4KQY.

10 new structures in release 1.9: 4BW0, 4C7O, 4JRC, 4K27, 4K31, 4KYY, 4L8H, 4LCK, 4LGT, 4MGN.

Obsolete: 2XZM4V5O, 3NPB4KQY.

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

Loading the Sankey diagram...

Changes in motif groups

Release 1.1 has 271 motif groups, release 1.9 has 271 motif groups, 175 of them are identical.

49 motif groups were updated, 47 groups are present only in release 1.1, 47 groups are only in release 1.9.

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_56465.346Single, unpaired intercalated base, consensus A
2IL_92027.31716S h21 S8 binding site
3IL_85647.316Sarcin-ricin parent motif with 15 Nts
4IL_90459.39cWW AG or UU
5IL_47444.39SRP Loop E-like motif
6IL_92114.39GAAA loop receptor "platform" motif
7IL_73000.27cHS-cWS
8IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
9IL_72158.36LSU Helix 62 (H62) IL
10IL_13069.36LSU 3WJ H32-H33-H35A
11IL_97057.36
12IL_25230.36Bacterial 5S rRNA Loop E
13IL_70237.36
14IL_53635.36LSU Helix 32 (H32) IL
15IL_79083.35
16IL_86357.35LSU Helix 61 IL2
17IL_02359.35
18IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
19IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
20IL_98591.34
21IL_01080.14
22IL_21333.24tSH-tHW-bulge
23IL_38807.34
24IL_22732.14tSH-inserted-tHS
25IL_34363.24Kink-turn from 23S H42
26IL_42251.14
27IL_39526.44
28IL_37053.13Kink-turn from 23S H58
29IL_43946.13
30IL_52173.13
31IL_82563.13Thi-box riboswitch T-loop
32IL_58586.23
33IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
34IL_05723.13
35IL_79955.23SSU Helix (23) h23 IL1
36IL_75447.13
37IL_80494.23LSU H58 IL2 H.m.
38IL_34628.23Kink-turn
39IL_12211.12
40IL_19898.12
41IL_23414.12
42IL_50521.12
43IL_90057.12
44IL_37197.12
45IL_45794.12
46IL_65137.12Kink-turn like motif in Group I Intron
47IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
48IL_94744.12Sarcin-ricin motif with extra cWW GA pair
49IL_00998.12
50IL_09587.12
51IL_31707.12Vitamin B12 aptamer
52IL_37406.12
53IL_40892.12
54IL_46435.12
55IL_55287.12
56IL_69536.12LSU Helix 96 (H96) IL2
57IL_09882.12
58IL_15840.22Triple Sheared with unpaired, inserted A
59IL_52940.12
60IL_80093.12
61IL_16330.12
62IL_21495.12
63IL_33964.12
64IL_76095.32Motif from Hairpin Ribozyme
65IL_87548.12
66IL_97833.12
67IL_11751.12
68IL_23262.42
69IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
70IL_77076.12
71IL_98566.12
72IL_03282.11
73IL_06847.11Group II Intron IL
74IL_28644.11
75IL_53988.11
76IL_57977.11
77IL_64589.11
78IL_77296.11
79IL_81398.11
80IL_03741.11
81IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
82IL_12507.11
83IL_20775.11tSH-inserted
84IL_23639.11tWH-tHS-L-cWW
85IL_30067.11
86IL_40527.11Kink-turn
87IL_54450.11
88IL_58454.11
89IL_85805.11
90IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
91IL_05221.11
92IL_09491.11
93IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
94IL_25082.11
95IL_30354.11
96IL_37347.11
97IL_40845.11
98IL_46306.11
99IL_52509.11
100IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
101IL_66744.11SSU Helix 21 (h21) IL2 E.coli
102IL_82601.11Tandem cWW water-inserted CU pairs
103IL_86059.11
104IL_91044.11
105IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
106IL_98924.11
107IL_15205.11
108IL_25181.11
109IL_52610.11
110IL_59529.11
111IL_75415.11Pseudo-knot forming internal loop
112IL_82650.11
113IL_91078.11
114IL_06306.11
115IL_21421.11
116IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
117IL_37990.11
118IL_41139.11
119IL_46721.11
120IL_55649.11
121IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
122IL_83250.1116S h40 3WJ T.th.
123IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
124IL_91089.11
125IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
126IL_02835.11
127IL_06468.1116S h40 3WJ E.c.
128IL_11302.11
129IL_25307.11
130IL_41791.11
131IL_52958.11
132IL_60649.11Kink-turn
133IL_83856.11
134IL_91904.11
135IL_02957.11
136IL_06471.11
137IL_17603.11
138IL_26868.11
139IL_39324.11
140IL_47687.11
141IL_53323.11
142IL_56513.11
143IL_61730.11
144IL_71685.11Sarcin-like with an intercalated basepair
145IL_76486.11Sarcin-ricin motif with syn G
146IL_80505.11
147IL_83920.11
148IL_88367.11
149IL_97842.11
150IL_03110.11
151IL_06808.11Double sheared (tSH-tSH) one bulged base.
152IL_11778.11
153IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
154IL_26971.11
155IL_43316.11
156IL_47732.11
157IL_63952.11
158IL_71942.11
159IL_80652.11
160IL_85510.11
161IL_89794.11

Updated motif groups

#Motif idInstancesDescription
1IL_39199.453Hoogsteen-edge Platform, Single bulged base
2IL_44540.443Sugar-edge, 1-base platform, consensus tHS
3IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
4IL_13959.426Double Sheared (tSH-tHS)
5IL_28947.22223S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
6IL_93424.421tSH-inserted-tHW
7IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
8IL_94430.51616S h32-h33-h34 3WJ
9IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
10IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
11IL_31555.413Tandem sheared with inserted, unpaired purine.
12IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
13IL_43124.21123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
14IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
15IL_58291.410Recurrent Sub-motif found in junctions
16IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
17IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
18IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
19IL_77263.26Kink-turn from U4
20IL_08926.3623S H91 IL
21IL_90133.36
22IL_25300.2616S h19 IL and 23S H41 IL
23IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
24IL_28572.2416S h18 kink-turn like motif
25IL_45262.44
26IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_82188.24LSU H68 IL from H.m.
28IL_31066.34SSU Helix 44 (h44) extension
29IL_48918.34Kink-turn variant
30IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
31IL_16166.4323S H91 IL
32IL_30840.23
33IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
34IL_98421.43SSU Helix 12 (h12) IL
35IL_07300.23
36IL_89028.63Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
37IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
38IL_09348.63Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
39IL_62499.73
40IL_09520.32Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
41IL_80348.2223S H91 IL

Removed motif groups

#Motif idInstancesDescription
1IL_06390.326cWH basepair with syn base
2IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_40090.31116S h34 ILa : Part of larger motif
4IL_54420.16
5IL_92484.15
6IL_16207.15Single sheared with bulged bases
7IL_78732.35Double S-turn motif
8IL_71565.24
9IL_08559.14LSU Helix 89 (H89) IL2
10IL_34156.63cWW AG or UU
11IL_56077.13
12IL_10647.13tHS tHH bulge with S-turn
13IL_92267.1323S H73 ILa : Part of larger Motif
14IL_70280.12Double sheared with wobble cWW.
15IL_28942.12
16IL_49550.12tHS tHH bulge with S-turn
17IL_16252.3223S H91 IL
18IL_33925.12
19IL_09901.12tHS tHH bulge with S-turn
20IL_01054.12
21IL_88180.12cWW-bulge-cWW
22IL_24358.12
23IL_89231.12LSU H77
24IL_27892.12
25IL_04550.11tHS tHH bulge with S-turn
26IL_13682.11
27IL_28468.11Single sheared with bulged bases
28IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
29IL_92280.11
30IL_05462.11
31IL_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.
32IL_31290.11
33IL_95774.11tHS tHH bulge with S-turn
34IL_54576.11
35IL_78809.11
36IL_97073.11
37IL_21221.11SSU Helix 12 (h12) IL
38IL_82113.11
39IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
40IL_60643.11
41IL_02690.11
42IL_12486.11
43IL_37715.11
44IL_65788.11
45IL_03931.1116S h19 IL and 23S H41 IL
46IL_13434.11
47IL_67735.11

Added motif groups

#Motif idInstancesDescription
1IL_82444.129cWH basepair with syn base | cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
2IL_37104.211Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_17212.110cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
4IL_25380.16LSU Helix 89 (H89) IL2
5IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
6IL_94403.54LSU H77
7IL_09530.14Double S-turn motif
8IL_39980.14
9IL_15709.14Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
10IL_31663.1423S H73 ILa : Part of larger Motif
11IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
12IL_06180.13tHS tHH bulge with S-turn
13IL_96206.23
14IL_87065.1323S H91 IL | Single-Base Intercalation Site
15IL_28003.13
16IL_46034.23
17IL_21639.12
18IL_74214.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
19IL_22358.12
20IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
21IL_85015.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases | Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_97509.12Double sheared with wobble cWW.
23IL_67887.12
24IL_87507.12tHS tHH bulge with S-turn
25IL_30381.12tHS tHH bulge with S-turn
26IL_47475.12LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
27IL_68880.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
28IL_90735.12
29IL_06177.11cWW AG or UU
30IL_49976.11
31IL_50911.1116S h34 ILa : Part of larger motif
32IL_95980.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
33IL_06421.11Single sheared with bulged bases
34IL_22909.11
35IL_54470.11tHS tHH bulge with S-turn
36IL_57364.11LSU Helix 89 (H89) IL2
37IL_41153.11
38IL_02897.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
39IL_68767.11
40IL_87523.11
41IL_05513.11
42IL_18675.11cWW-bulge-cWW
43IL_31224.1123S H91 IL
44IL_88119.11
45IL_21077.11
46IL_49527.11
47IL_69799.11
Copyright 2024 BGSU RNA group. Page generated in 0.1985 s