Changes in PDB files used for clustering

Release 1.17 has 243 PDB files, release 1.18 has 246 PDB files, 240 of them are identical.

1 equivalence classes changed representatives: 4LCK4TZZ.

5 new structures in release 1.18: 4PDB, 4QJH, 4R0D, 4W21, 4W23.

Obsolete: 1VWW4W1Z, 1VX24W28.

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 1.17 has 364 motif groups, release 1.18 has 372 motif groups, 193 of them are identical.

75 motif groups were updated, 96 groups are present only in release 1.17, 104 groups are only in release 1.18.

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_67038.11523S H91 IL | Single-Base Intercalation Site
2IL_18271.112Single, unpaired intercalated base, consensus A | 23S H91 IL
3IL_53635.69LSU Helix 32 (H32) IL
4IL_64847.27Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
5IL_15123.36Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
6IL_51439.16
7IL_25230.56Bacterial 5S rRNA Loop E
8IL_02359.66
9IL_98421.75SSU Helix 12 (h12) IL | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
10IL_71229.25
11IL_39980.25
12IL_55114.35Double S-turn motif | tHS tHH bulge with S-turn | Double S-turn motif
13IL_04397.25
14IL_32508.1423S H91 IL
15IL_43727.14tSH-inserted-tHS | tHS tHH bulge with S-turn | tSH-inserted-tHS
16IL_94519.24
17IL_16166.5423S H91 IL
18IL_77076.34
19IL_39526.44
20IL_48918.34Kink-turn variant
21IL_83339.14
22IL_98073.23Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
23IL_21639.23
24IL_34628.23Kink-turn
25IL_40892.23
26IL_43946.13
27IL_22025.13
28IL_82563.13Thi-box riboswitch T-loop
29IL_19268.13
30IL_62499.10323S H91 IL
31IL_45592.2323S H91 IL
32IL_28003.22
33IL_28028.12
34IL_43363.12
35IL_46435.12
36IL_76095.32Motif from Hairpin Ribozyme
37IL_91942.12
38IL_98172.12
39IL_21495.12
40IL_28058.12
41IL_33842.12
42IL_39175.12
43IL_65137.12Kink-turn like motif in Group I Intron
44IL_70401.12
45IL_09882.12
46IL_52940.12
47IL_94744.12Sarcin-ricin motif with extra cWW GA pair
48IL_06675.12Triple Sheared with unpaired, inserted A
49IL_16330.12
50IL_39439.12
51IL_44092.12
52IL_67024.12
53IL_03362.12
54IL_06692.12
55IL_44977.12LSU H58 IL2 H.m. | SSU Helix (23) h23 IL1
56IL_31707.12Vitamin B12 aptamer
57IL_35558.12
58IL_68034.12
59IL_21062.12Sarcin-ricin motif with cWW UU instead of tSH basepair.
60IL_23414.12
61IL_40041.12
62IL_50521.12
63IL_74462.12
64IL_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.
65IL_05221.11
66IL_07252.11
67IL_21077.11
68IL_23639.11tWH-tHS-L-cWW
69IL_37347.11
70IL_40364.11
71IL_42891.11
72IL_45617.11
73IL_57334.11
74IL_63952.11
75IL_69482.11
76IL_75415.11Pseudo-knot forming internal loop
77IL_80652.11
78IL_84276.11
79IL_87523.11
80IL_91089.11
81IL_02957.11
82IL_05513.11
83IL_08588.11
84IL_15205.11
85IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
86IL_33217.11
87IL_37970.11tHS tHH bulge with S-turn | tSH-inserted-tHS
88IL_40527.11Kink-turn
89IL_51572.11
90IL_57977.11
91IL_70069.11tHS tHH bulge with S-turn
92IL_80714.11
93IL_84995.11
94IL_88367.11
95IL_03030.11tSH-inserted-tHS
96IL_06306.11
97IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
98IL_15884.11
99IL_25420.11
100IL_40845.11
101IL_47687.11
102IL_52610.11
103IL_58270.11
104IL_76263.11
105IL_81280.11
106IL_85510.11
107IL_89463.11
108IL_00346.11
109IL_03110.11
110IL_06468.1116S h40 3WJ E.c.
111IL_25808.11
112IL_28644.11
113IL_39324.11
114IL_47702.11
115IL_59907.11
116IL_66744.11SSU Helix 21 (h21) IL2 E.coli
117IL_70529.11
118IL_81587.11
119IL_86059.11
120IL_89794.11
121IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
122IL_01562.11
123IL_03282.11
124IL_11268.11
125IL_25926.11
126IL_29058.11
127IL_34816.11
128IL_41139.11
129IL_48036.11
130IL_52958.11
131IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
132IL_77296.11
133IL_86060.11
134IL_90633.11
135IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
136IL_98924.11
137IL_02257.11
138IL_11302.11
139IL_22909.11
140IL_26868.11
141IL_31160.11
142IL_35267.11
143IL_41215.11
144IL_48268.11
145IL_62296.11
146IL_73656.11
147IL_77862.11
148IL_82601.11Tandem cWW water-inserted CU pairs
149IL_86336.11
150IL_91044.11
151IL_96591.11
152IL_99784.11
153IL_03808.11
154IL_06808.11Double sheared (tSH-tSH) one bulged base.
155IL_11778.11
156IL_22953.11Single 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) | Single 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) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
157IL_26971.11
158IL_41371.11
159IL_45432.11
160IL_74400.11
161IL_79910.11
162IL_82650.11
163IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
164IL_91061.11
165IL_97803.11
166IL_99937.11
167IL_02835.11
168IL_06847.11Group II Intron IL
169IL_12507.11
170IL_27640.11
171IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
172IL_36006.11
173IL_41516.11
174IL_55649.11
175IL_62617.11
176IL_68827.11Reverse Kink-Turn
177IL_80505.11
178IL_87394.11
179IL_91078.11
180IL_97842.11

Updated motif groups

#Motif idInstancesDescription
1IL_48256.23711-3 bulged nucleotides, same chain | 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 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | 23S 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 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 1-3 bulged nucleotides
2IL_92602.2321Non-canonical cWW basepair
3IL_41766.1088Stacked cWW-cWH pairs | Tandem cWW pairs (Not AU or GC)
4IL_39199.874Hoogsteen-edge Platform, Single bulged base
5IL_67828.26523S H91 IL | Single-Base Intercalation Site | Single, unpaired intercalated base, consensus A | 16S h32-h33-h34 3WJ
6IL_44540.862One or more bulged nucleotides | Sugar-edge, 1-base platform, consensus tHS
7IL_13959.839Double Sheared (tSH-tHS)
8IL_82822.235One or more bulged bases
9IL_73276.931C-loop
10IL_93424.831tSH-inserted-tHW
11IL_65553.1229Kink-turn
12IL_55938.827LSU Helix 89 (H89) IL2. cSH Platform.
13IL_85647.725Sarcin-ricin parent motif with 15 Nts
14IL_92027.72516S h21 S8 binding site
15IL_34098.221cWW with bulged base | tHS and base triple with flanking pair
16IL_37104.719Single sheared with bulged bases
17IL_49493.818Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_53587.218Base triple, intercalated pair, and bulged bases making long-range interactions. | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
19IL_37964.216Recurrent Sub-motif found in junctions
20IL_31555.815Tandem sheared with inserted, unpaired purine
21IL_19986.215Pair and triple
22IL_58261.213SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
23IL_92114.511GAAA loop receptor "platform" motif
24IL_02809.510REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
25IL_92122.210
26IL_11015.310tHS and base triple with flanking pair
27IL_13069.79LSU 3WJ H32-H33-H35A
28IL_32902.29Stacked cWW-cWH pairs
29IL_70237.79
30IL_86933.29Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
31IL_72158.79LSU Helix 62 (H62) IL
32IL_12849.28
33IL_89033.2823S H41 IL and 16S h18 IL : Has large bulge on one side
34IL_74856.48LSU Helix 89 (H89) IL2
35IL_39212.28
36IL_31066.67SSU Helix 44 (h44) extension
37IL_82188.57LSU H68 IL from H.m.
38IL_93568.67Triple Sheared (tSH-tHS-tHS) with wobble cWW.
39IL_95652.67SSU Helix 27 (h27) IL Sarcin-Ricin motif
40IL_08926.6723S H91 IL
41IL_77263.37Kink-turn from U4
42IL_73000.47cHS-cWS
43IL_32261.46LSU Helix 89 (H89) IL2
44IL_85010.2623S H91 IL | Single-Base Intercalation Site
45IL_98016.26One or more bulged nucleotides
46IL_34363.46Kink-turn from 23S H42
47IL_26321.26LSU H58 IL2 H.m. | SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
48IL_28572.5616S h18 kink-turn like motif
49IL_73281.25Sarcin-like with an intercalated basepair
50IL_15702.25
51IL_86694.25SSU Helix 8 (h8) IL E.c. and Yeast | LSU H68 IL from H.m.
52IL_99363.25
53IL_37053.45Kink-turn from 23S H58
54IL_60760.25
55IL_12211.45
56IL_37197.44
57IL_94403.74LSU H77
58IL_69536.54LSU Helix 96 (H96) IL2
59IL_70089.24
60IL_40053.24
61IL_90735.33
62IL_91102.23
63IL_74876.43Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
64IL_09530.43Double S-turn motif
65IL_78744.23Quadruple Sheared (tSH-tSH-tHS-tHS)
66IL_87548.23
67IL_92205.23cWW AG or water inserted cWW Y-Y. | Single 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)
68IL_87899.23SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
69IL_63917.22
70IL_37914.32
71IL_24955.22
72IL_59563.32Sarcin-ricin motif with syn G
73IL_79398.22cWW 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
74IL_62504.22Triple Sheared with unpaired, inserted A
75IL_80494.52LSU H58 IL2 H.m.

Removed motif groups

#Motif idInstancesDescription
1IL_81965.144Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW.
2IL_82444.442cWH basepair
3IL_24982.821SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
4IL_68200.118One or more bulged nucleotides
5IL_94430.81516S h32-h33-h34 3WJ
6IL_49203.114Double sheared with wobble cWW.
7IL_27005.112Non-canonical cWW
8IL_65542.110SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
9IL_86357.69LSU Helix 61 IL2
10IL_38078.19
11IL_51342.18Non-canonical cWW with inserted stacked base.
12IL_18916.17One or more bulged nucleotides
13IL_10743.16
14IL_67399.16REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
15IL_31772.16SRP Loop E-like motif | SSU Helix (23) h23 IL1
16IL_77920.16
17IL_01551.16
18IL_72062.15
19IL_52024.15
20IL_37688.15Stacked bases not quite making a basepair.
21IL_10554.15SSU Helix 23 (h23) Kink-turn T. thermophilus
22IL_59276.15
23IL_50787.14tSH-tHW-bulge
24IL_62615.14cWS plus stacked base
25IL_13023.14
26IL_00520.14
27IL_45593.14
28IL_61513.14One or more bulged nucleotides
29IL_17204.23
30IL_74163.13cWS making long-range triple
31IL_82600.13cWW 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
32IL_14081.13Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
33IL_48070.13C-loop
34IL_01827.13Base triple, intercalated pair, and bulged bases making long-range interactions.
35IL_86033.12
36IL_06413.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
37IL_67005.12
38IL_73348.12Triple sheared (tSH-tHS-tHS) no inserted bases
39IL_94799.12tHS tHH bulge with S-turn
40IL_06527.12
41IL_51576.12
42IL_07300.32
43IL_44847.12
44IL_64894.1223S H91 IL | Single-Base Intercalation Site
45IL_68945.12
46IL_88416.12
47IL_00697.12
48IL_10119.12
49IL_69668.12
50IL_92422.12
51IL_79636.12Kink-turn
52IL_24583.12
53IL_38488.12
54IL_06177.11cWW AG or UU
55IL_39296.11
56IL_62008.11
57IL_66775.11
58IL_81956.11
59IL_11529.11
60IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
61IL_40987.1123S H91 IL | Single-Base Intercalation Site
62IL_11989.11
63IL_18506.11
64IL_27713.11
65IL_41027.11
66IL_63366.11
67IL_87168.11
68IL_94958.11
69IL_00519.11Triple sheared (tSH-tHS-tHS) no inserted bases
70IL_41920.11
71IL_63723.11
72IL_76024.11
73IL_88263.11
74IL_09430.11
75IL_20608.11
76IL_34548.11
77IL_55210.111-3 bulged nucleotides, same chain | 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 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | 23S 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 | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
78IL_83250.1116S h40 3WJ T.th.
79IL_14240.11
80IL_22601.11
81IL_57625.11
82IL_78984.11
83IL_85707.11
84IL_15219.11
85IL_22731.11
86IL_65681.11
87IL_70102.11
88IL_85805.11
89IL_92957.11
90IL_10628.11
91IL_15813.11
92IL_66407.11
93IL_72055.11
94IL_81512.11
95IL_85975.11
96IL_92986.11

Added motif groups

#Motif idInstancesDescription
1IL_37976.144Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | Triple sheared (tSH-tHS-tHS) no inserted bases | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
2IL_85638.143cWH basepair | Non-canonical cWW basepair | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
3IL_77895.120Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
4IL_21137.118Sugar-edge, 1-base platform, consensus tHS | cHS-cWS | 16S h32-h33-h34 3WJ
5IL_66381.117One or more bulged nucleotides | 1-3 bulged nucleotides | 23S H41 IL and 16S h18 IL : Has large bulge on one side
6IL_68859.116Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | Double sheared with wobble cWW.
7IL_93635.113Non-canonical cWW
8IL_68638.112One or more bulged nucleotides
9IL_75508.112LSU Helix 61 IL2 | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
10IL_98284.19SRP Loop E-like motif | SSU Helix (23) h23 IL1 | SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
11IL_72032.18LSU Helix 96 (H96) IL2
12IL_96532.17cWS plus stacked base
13IL_74753.16Non-canonical cWW with inserted stacked base.
14IL_22529.16cWW AG or UU | cWW 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 | Stacked bases not quite making a basepair. | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
15IL_41366.16
16IL_99561.16Double Sheared (tSH-tHS) | Stacked cWW-cWH pairs | tSH-tHW-bulge
17IL_07837.15Non-canonical cWW with inserted stacked base. | cWS plus stacked base | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
18IL_04238.15cWH basepair | Stacked bases not quite making a basepair.
19IL_70108.15REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
20IL_84284.15
21IL_99840.15Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | Triple sheared (tSH-tHS-tHS) no inserted bases
22IL_06584.14
23IL_52184.14Base triple, intercalated pair, and bulged bases making long-range interactions.
24IL_10822.14cWS making long-range triple
25IL_92942.14cWW 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
26IL_04466.14
27IL_77152.14
28IL_77382.14SRP Loop E-like motif | SSU Helix (23) h23 IL1
29IL_96898.13
30IL_53504.13
31IL_68139.13One or more bulged nucleotides
32IL_75951.13Non-canonical cWW with inserted stacked base. | cWS plus stacked base
33IL_84401.13cWW with bulged base
34IL_28666.12
35IL_37481.12
36IL_51413.12Sarcin-ricin motif from Eukaryal LSU Helix 11
37IL_77809.12C-loop
38IL_22165.12
39IL_32815.12REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
40IL_57674.12
41IL_92630.12tHS tHH bulge with S-turn
42IL_79341.12Non-canonical cWW basepair
43IL_86090.12
44IL_03783.12
45IL_34637.12
46IL_81791.12
47IL_35279.12
48IL_58695.12
49IL_87433.12
50IL_19589.12
51IL_22611.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
52IL_41740.12
53IL_93090.12
54IL_20094.12
55IL_37400.12SSU Helix 23 (h23) Kink-turn T. thermophilus
56IL_55583.1223S H91 IL | Single-Base Intercalation Site | 16S h32-h33-h34 3WJ
57IL_27536.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
58IL_70320.1216S h40 3WJ T.th.
59IL_21577.11LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
60IL_56616.11
61IL_84773.11
62IL_92115.11
63IL_66408.11
64IL_96604.11
65IL_22247.11
66IL_33156.11
67IL_39044.11
68IL_53415.1123S H91 IL
69IL_57780.11
70IL_67360.11
71IL_75176.11
72IL_92733.11
73IL_12192.11
74IL_22368.11
75IL_40852.11
76IL_58203.11cWH basepair
77IL_75231.1116S h32-h33-h34 3WJ
78IL_86167.11
79IL_04023.11
80IL_14652.11
81IL_54405.11
82IL_83427.11
83IL_93035.11
84IL_36321.11
85IL_54542.11
86IL_58965.11
87IL_83917.11
88IL_87776.11
89IL_99739.11
90IL_24658.11
91IL_45126.11
92IL_60334.11
93IL_90660.11
94IL_05920.11One or more bulged nucleotides
95IL_37408.11Kink-turn from 23S H58
96IL_48045.11
97IL_56083.11
98IL_64749.11
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