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

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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_13069.36LSU 3WJ H32-H33-H35A
12IL_25230.36Bacterial 5S rRNA Loop E
13IL_70237.36
14IL_72158.36LSU Helix 62 (H62) IL
15IL_97057.36
16IL_53635.36LSU Helix 32 (H32) IL
17IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
18IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
19IL_02359.35
20IL_79083.35
21IL_86357.35LSU Helix 61 IL2
22IL_25300.1516S h19 IL and 23S H41 IL
23IL_42251.14
24IL_39526.44
25IL_38807.34
26IL_34363.24Kink-turn from 23S H42
27IL_98591.34
28IL_01080.14
29IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
30IL_22732.14tSH-inserted-tHS
31IL_21333.24tSH-tHW-bulge
32IL_80494.23LSU H58 IL2 H.m.
33IL_75447.13
34IL_80348.1323S H91 IL
35IL_52173.13
36IL_05723.13
37IL_37053.13Kink-turn from 23S H58
38IL_82563.13Thi-box riboswitch T-loop
39IL_43946.13
40IL_34628.23Kink-turn
41IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42IL_58586.23
43IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
44IL_48918.23Kink-turn variant
45IL_79955.23SSU Helix (23) h23 IL1
46IL_11751.12
47IL_97833.12
48IL_45794.12
49IL_76095.32Motif from Hairpin Ribozyme
50IL_12211.12
51IL_16330.12
52IL_50521.12
53IL_09587.12
54IL_37406.12
55IL_40892.12
56IL_87548.12
57IL_21495.12
58IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
59IL_52940.12
60IL_09882.12
61IL_77076.12
62IL_23262.42
63IL_31707.12Vitamin B12 aptamer
64IL_90057.12
65IL_98566.12
66IL_01054.12
67IL_15840.22Triple Sheared with unpaired, inserted A
68IL_55287.12
69IL_19898.12
70IL_46435.12
71IL_94744.12Sarcin-ricin motif with extra cWW GA pair
72IL_65137.12Kink-turn like motif in Group I Intron
73IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
74IL_80093.12
75IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
76IL_00998.12
77IL_69536.12LSU Helix 96 (H96) IL2
78IL_23414.12
79IL_37197.12
80IL_33964.12
81IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
82IL_43316.11
83IL_80505.11
84IL_66744.11SSU Helix 21 (h21) IL2 E.coli
85IL_52509.11
86IL_78809.11
87IL_75415.11Pseudo-knot forming internal loop
88IL_76486.11Sarcin-ricin motif with syn G
89IL_37990.11
90IL_17603.11
91IL_85510.11
92IL_60649.11Kink-turn
93IL_47732.11
94IL_40845.11
95IL_57977.11
96IL_82650.11
97IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
98IL_52958.11
99IL_54576.11
100IL_03741.11
101IL_97842.11
102IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
103IL_56513.11
104IL_88367.11
105IL_77296.11
106IL_30354.11
107IL_85805.11
108IL_92280.11
109IL_41791.11
110IL_25307.11
111IL_11778.11
112IL_91078.11
113IL_37347.11
114IL_46306.11
115IL_21421.11
116IL_40527.11Kink-turn
117IL_03282.11
118IL_46721.11
119IL_83250.1116S h40 3WJ T.th.
120IL_03110.11
121IL_76263.11
122IL_83920.11
123IL_06468.1116S h40 3WJ E.c.
124IL_55649.11
125IL_20775.11tSH-inserted
126IL_06306.11
127IL_05221.11
128IL_06471.11
129IL_91904.11
130IL_58454.11
131IL_41139.11
132IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
133IL_63952.11
134IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
135IL_68827.11Reverse Kink-Turn
136IL_47687.11
137IL_28644.11
138IL_06808.11Double sheared (tSH-tSH) one bulged base.
139IL_71942.11
140IL_83856.11
141IL_53323.11
142IL_26971.11
143IL_09491.11
144IL_64589.11
145IL_91089.11
146IL_30067.11
147IL_39324.11
148IL_86059.11
149IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
150IL_89794.11
151IL_80652.11
152IL_54450.11
153IL_81398.11
154IL_98924.11
155IL_59529.11
156IL_02957.11
157IL_82601.11Tandem cWW water-inserted CU pairs
158IL_60643.11
159IL_52610.11
160IL_02835.11
161IL_26868.11
162IL_53988.11
163IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
164IL_13682.11
165IL_25082.11
166IL_71685.11Sarcin-like with an intercalated basepair
167IL_25181.11
168IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
169IL_91044.11
170IL_87394.11
171IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
172IL_12507.11
173IL_11302.11
174IL_61730.11
175IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
176IL_23639.11tWH-tHS-L-cWW
177IL_15205.11
178IL_06847.11Group II Intron IL
179IL_42891.11

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_73276.421C-loop
10IL_93424.421tSH-inserted-tHW
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_49493.413Sarcin-ricin Parent Motif - bacterial LSU H95 IL
16IL_31555.413Tandem sheared with inserted, unpaired purine.
17IL_40090.510Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
18IL_24546.41023S H41 IL and 16S h18 IL : Has large bulge on one side
19IL_58291.410Recurrent Sub-motif found in junctions
20IL_46648.31023S H91 IL | Single-Base Intercalation Site
21IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
22IL_83451.37cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
23IL_90133.36
24IL_77263.26Kink-turn from U4
25IL_08926.3623S H91 IL
26IL_44067.45Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
27IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
28IL_31066.34SSU Helix 44 (h44) extension
29IL_45262.44
30IL_28572.2416S h18 kink-turn like motif
31IL_82188.24LSU H68 IL from H.m.
32IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
33IL_71565.44
34IL_98421.43SSU Helix 12 (h12) IL
35IL_62499.73
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_16166.4323S H91 IL
38IL_30840.23
39IL_07300.23
40IL_95150.43
41IL_16415.23SSU Helix 23 (h23) Kink-turn T. thermophilus
42IL_94403.23LSU H77
43IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast

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_16207.15Single sheared with bulged bases
5IL_92484.15
6IL_78732.35Double S-turn motif
7IL_08559.14LSU Helix 89 (H89) IL2
8IL_56077.13
9IL_92267.1323S H73 ILa : Part of larger Motif
10IL_34156.63cWW AG or UU
11IL_10647.13tHS tHH bulge with S-turn
12IL_27892.12
13IL_49550.12tHS tHH bulge with S-turn
14IL_88180.12cWW-bulge-cWW
15IL_28942.12
16IL_91273.12
17IL_16252.3223S H91 IL
18IL_33925.12
19IL_09901.12tHS tHH bulge with S-turn
20IL_70280.12Double sheared with wobble cWW.
21IL_24358.12
22IL_02690.11
23IL_12486.11
24IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
25IL_82113.11
26IL_03931.1116S h19 IL and 23S H41 IL
27IL_13434.11
28IL_28468.11Single sheared with bulged bases
29IL_04550.11tHS tHH bulge with S-turn
30IL_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.
31IL_05462.11
32IL_31290.11
33IL_65788.11
34IL_21221.11SSU Helix 12 (h12) IL
35IL_67735.11
36IL_95774.11tHS tHH bulge with S-turn
37IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
38IL_97073.11
39IL_37715.11

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_97509.12Double sheared with wobble cWW.
13IL_35595.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases
14IL_35994.12cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
15IL_87507.12tHS tHH bulge with S-turn
16IL_21639.12
17IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
18IL_67887.12
19IL_90735.12
20IL_30381.12tHS tHH bulge with S-turn
21IL_46034.12
22IL_12685.12cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_96206.12
24IL_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.
25IL_49976.11
26IL_18675.11cWW-bulge-cWW
27IL_50911.1116S h34 ILa : Part of larger motif
28IL_99438.11
29IL_06177.11cWW AG or UU
30IL_20530.11
31IL_54470.11tHS tHH bulge with S-turn
32IL_21077.11
33IL_57364.11LSU Helix 89 (H89) IL2
34IL_87523.11
35IL_59018.11
36IL_88119.11
37IL_06421.11Single sheared with bulged bases
38IL_68767.11
39IL_96182.11cWH basepair with syn base
40IL_31224.1123S H91 IL
41IL_49527.11
42IL_69799.11