Changes in PDB files used for clustering

Release 1.4 has 201 PDB files, release 1.5 has 203 PDB files, 200 of them are identical.

1 equivalence classes changed representatives: 2XZM4BPP.

2 new structures in release 1.5: 4K31, 4LCK.

Obsolete: 2XZM4V5O.

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 1.4 has 271 motif groups, release 1.5 has 274 motif groups, 189 of them are identical.

43 motif groups were updated, 39 groups are present only in release 1.4, 42 groups are only in release 1.5.

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_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_92027.31716S h21 S8 binding site
4IL_85647.316Sarcin-ricin parent motif with 15 Nts
5IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
6IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
7IL_92114.39GAAA loop receptor "platform" motif
8IL_47444.39SRP Loop E-like motif
9IL_90459.39cWW AG or UU
10IL_73000.27cHS-cWS
11IL_53635.36LSU Helix 32 (H32) IL
12IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
13IL_13069.36LSU 3WJ H32-H33-H35A
14IL_25230.36Bacterial 5S rRNA Loop E
15IL_70237.36
16IL_72158.36LSU Helix 62 (H62) IL
17IL_97057.36
18IL_79083.35
19IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
20IL_86357.35LSU Helix 61 IL2
21IL_25300.1516S h19 IL and 23S H41 IL
22IL_02359.35
23IL_21333.24tSH-tHW-bulge
24IL_39526.44
25IL_42251.14
26IL_38807.34
27IL_34363.24Kink-turn from 23S H42
28IL_98591.34
29IL_01080.14
30IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
31IL_22732.14tSH-inserted-tHS
32IL_79955.23SSU Helix (23) h23 IL1
33IL_82563.13Thi-box riboswitch T-loop
34IL_80494.23LSU H58 IL2 H.m.
35IL_34628.23Kink-turn
36IL_80348.1323S H91 IL
37IL_52173.13
38IL_05723.13
39IL_37053.13Kink-turn from 23S H58
40IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
41IL_43946.13
42IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
43IL_48918.23Kink-turn variant
44IL_58586.23
45IL_75447.13
46IL_65137.12Kink-turn like motif in Group I Intron
47IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
48IL_80093.12
49IL_16330.12
50IL_11751.12
51IL_97833.12
52IL_09587.12
53IL_37406.12
54IL_40892.12
55IL_76095.32Motif from Hairpin Ribozyme
56IL_12211.12
57IL_21495.12
58IL_50521.12
59IL_23262.42
60IL_87548.12
61IL_01054.12
62IL_15840.22Triple Sheared with unpaired, inserted A
63IL_55287.12
64IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
65IL_52940.12
66IL_09882.12
67IL_77076.12
68IL_46435.12
69IL_94744.12Sarcin-ricin motif with extra cWW GA pair
70IL_31707.12Vitamin B12 aptamer
71IL_90057.12
72IL_98566.12
73IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
74IL_00998.12
75IL_69536.12LSU Helix 96 (H96) IL2
76IL_23414.12
77IL_37197.12
78IL_33964.12
79IL_19898.12
80IL_45794.12
81IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
82IL_82650.11
83IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
84IL_52958.11
85IL_54576.11
86IL_03741.11
87IL_97842.11
88IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
89IL_56513.11
90IL_88367.11
91IL_77296.11
92IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
93IL_43316.11
94IL_25307.11
95IL_11778.11
96IL_91078.11
97IL_37347.11
98IL_46306.11
99IL_21421.11
100IL_40527.11Kink-turn
101IL_03282.11
102IL_40845.11
103IL_57977.11
104IL_83920.11
105IL_06468.1116S h40 3WJ E.c.
106IL_55649.11
107IL_20775.11tSH-inserted
108IL_06306.11
109IL_05221.11
110IL_06471.11
111IL_91904.11
112IL_58454.11
113IL_41139.11
114IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
115IL_85805.11
116IL_92280.11
117IL_41791.11
118IL_47687.11
119IL_28644.11
120IL_06808.11Double sheared (tSH-tSH) one bulged base.
121IL_71942.11
122IL_83856.11
123IL_53323.11
124IL_26971.11
125IL_09491.11
126IL_64589.11
127IL_91089.11
128IL_30067.11
129IL_83250.1116S h40 3WJ T.th.
130IL_03110.11
131IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
132IL_89794.11
133IL_80652.11
134IL_54450.11
135IL_81398.11
136IL_98924.11
137IL_59529.11
138IL_02957.11
139IL_82601.11Tandem cWW water-inserted CU pairs
140IL_60643.11
141IL_52610.11
142IL_63952.11
143IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
144IL_26868.11
145IL_53988.11
146IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
147IL_13682.11
148IL_25082.11
149IL_71685.11Sarcin-like with an intercalated basepair
150IL_25181.11
151IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
152IL_91044.11
153IL_47732.11
154IL_39324.11
155IL_86059.11
156IL_12507.11
157IL_11302.11
158IL_61730.11
159IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
160IL_23639.11tWH-tHS-L-cWW
161IL_15205.11
162IL_06847.11Group II Intron IL
163IL_30354.11
164IL_02835.11
165IL_80505.11
166IL_66744.11SSU Helix 21 (h21) IL2 E.coli
167IL_52509.11
168IL_78809.11
169IL_75415.11Pseudo-knot forming internal loop
170IL_76486.11Sarcin-ricin motif with syn G
171IL_37990.11
172IL_17603.11
173IL_85510.11
174IL_60649.11Kink-turn
175IL_46721.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.72431-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.8205cWW AG or water inserted cWW Y-Y.
3IL_39199.453Hoogsteen-edge Platform, Single bulged base
4IL_41766.449Tandem cWW pairs (Not AU or GC)
5IL_44540.443Sugar-edge, 1-base platform, consensus tHS
6IL_87904.531Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_13959.426Double Sheared (tSH-tHS)
8IL_65553.622Kink-turn
9IL_93424.421tSH-inserted-tHW
10IL_73276.421C-loop
11IL_55938.418LSU Helix 89 (H89) IL2. cSH Platform.
12IL_24982.516SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
13IL_94430.51616S h32-h33-h34 3WJ
14IL_92109.215cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
15IL_31555.413Tandem sheared with inserted, unpaired purine.
16IL_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
17IL_46648.31023S H91 IL | Single-Base Intercalation Site
18IL_40090.510Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
19IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
20IL_58291.410Recurrent Sub-motif found in junctions
21IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
22IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
23IL_77263.26Kink-turn from U4
24IL_08926.3623S H91 IL
25IL_90133.36
26IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
27IL_28572.2416S h18 kink-turn like motif
28IL_82188.24LSU H68 IL from H.m.
29IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
30IL_71565.44
31IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_31066.34SSU Helix 44 (h44) extension
33IL_45262.44
34IL_95150.43
35IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
36IL_94403.23LSU H77
37IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
38IL_98421.43SSU Helix 12 (h12) IL
39IL_62499.73
40IL_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.
41IL_16166.4323S H91 IL
42IL_30840.23
43IL_07300.23

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_54420.16
4IL_78732.35Double S-turn motif
5IL_16207.15Single sheared with bulged bases
6IL_92484.15
7IL_08559.14LSU Helix 89 (H89) IL2
8IL_10647.13tHS tHH bulge with S-turn
9IL_56077.13
10IL_92267.1323S H73 ILa : Part of larger Motif
11IL_34156.63cWW AG or UU
12IL_24358.12
13IL_27892.12
14IL_49550.12tHS tHH bulge with S-turn
15IL_88180.12cWW-bulge-cWW
16IL_28942.12
17IL_91273.12
18IL_16252.3223S H91 IL
19IL_33925.12
20IL_09901.12tHS tHH bulge with S-turn
21IL_70280.12Double sheared with wobble cWW.
22IL_37715.11
23IL_02690.11
24IL_12486.11
25IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
26IL_82113.11
27IL_03931.1116S h19 IL and 23S H41 IL
28IL_13434.11
29IL_28468.11Single sheared with bulged bases
30IL_04550.11tHS tHH bulge with S-turn
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_05462.11
33IL_31290.11
34IL_65788.11
35IL_21221.11SSU Helix 12 (h12) IL
36IL_67735.11
37IL_95774.11tHS tHH bulge with S-turn
38IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
39IL_97073.11

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_37104.111Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3IL_25380.16LSU Helix 89 (H89) IL2
4IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
5IL_15768.14cWW AG or UU | cWH basepair with syn base
6IL_31663.1423S H73 ILa : Part of larger Motif
7IL_39980.14
8IL_09530.14Double S-turn motif
9IL_87065.1323S H91 IL | Single-Base Intercalation Site
10IL_06180.13tHS tHH bulge with S-turn
11IL_06211.13
12IL_12685.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
13IL_96206.12
14IL_97509.12Double sheared with wobble cWW.
15IL_35595.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases
16IL_35994.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
17IL_87507.12tHS tHH bulge with S-turn
18IL_21639.12
19IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
20IL_67887.12
21IL_90735.12
22IL_30381.12tHS tHH bulge with S-turn
23IL_46034.12
24IL_31224.1123S H91 IL
25IL_49527.11
26IL_69799.11
27IL_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.
28IL_49976.11
29IL_18675.11cWW-bulge-cWW
30IL_50911.1116S h34 ILa : Part of larger motif
31IL_99438.11
32IL_06177.11cWW AG or UU
33IL_20530.11
34IL_54470.11tHS tHH bulge with S-turn
35IL_21077.11
36IL_57364.11LSU Helix 89 (H89) IL2
37IL_87523.11
38IL_59018.11
39IL_88119.11
40IL_06421.11Single sheared with bulged bases
41IL_68767.11
42IL_96182.11cWH basepair with syn base