Changes in PDB files used for clustering

Release 1.0 has 200 PDB files, release 1.1 has 200 PDB files, 198 of them are identical.

1 equivalence classes changed representatives: 2ZJR4IOA.

1 new structures in release 1.1: 3ZP8.

Obsolete: 3ZD33ZP8.

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 1.0 has 267 motif groups, release 1.1 has 271 motif groups, 179 of them are identical.

51 motif groups were updated, 37 groups are present only in release 1.0, 41 groups are only in release 1.1.

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_31555.315Tandem sheared with inserted, unpaired purine.
2IL_47444.39SRP Loop E-like motif
3IL_92114.39GAAA loop receptor "platform" motif
4IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
5IL_73000.27cHS-cWS
6IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
7IL_70237.36
8IL_54420.16
9IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
10IL_78732.35Double S-turn motif
11IL_92484.15
12IL_77263.15Kink-turn from U4
13IL_25300.1516S h19 IL and 23S H41 IL
14IL_82188.15LSU H68 IL from H.m.
15IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
16IL_39526.44
17IL_28572.1416S h18 kink-turn like motif
18IL_31066.24SSU Helix 44 (h44) extension
19IL_22732.14tSH-inserted-tHS
20IL_71565.24
21IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
22IL_82563.13Thi-box riboswitch T-loop
23IL_43946.13
24IL_30840.13
25IL_52173.13
26IL_80494.23LSU H58 IL2 H.m.
27IL_34628.23Kink-turn
28IL_37053.13Kink-turn from 23S H58
29IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
30IL_95150.33
31IL_79955.23SSU Helix (23) h23 IL1
32IL_05723.13
33IL_58586.23
34IL_75447.13
35IL_76095.32Motif from Hairpin Ribozyme
36IL_98566.12
37IL_12211.12
38IL_55287.12
39IL_40892.12
40IL_96446.12
41IL_50521.12
42IL_65137.12Kink-turn like motif in Group I Intron
43IL_37406.12
44IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
45IL_87548.12
46IL_80093.12
47IL_28942.12
48IL_23414.12
49IL_89231.12LSU H77
50IL_21495.12
51IL_31707.12Vitamin B12 aptamer
52IL_52940.12
53IL_09882.12
54IL_77076.12
55IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
56IL_70280.12Double sheared with wobble cWW.
57IL_90057.12
58IL_46435.12
59IL_15840.22Triple Sheared with unpaired, inserted A
60IL_37197.12
61IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
62IL_01054.12
63IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
64IL_16252.3223S H91 IL
65IL_94744.12Sarcin-ricin motif with extra cWW GA pair
66IL_45794.12
67IL_11751.12
68IL_97833.12
69IL_00998.12
70IL_27892.12
71IL_07300.12
72IL_16330.12
73IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
74IL_82650.11
75IL_11302.11
76IL_52958.11
77IL_20775.11tSH-inserted
78IL_65788.11
79IL_61730.11
80IL_06306.11
81IL_37347.11
82IL_46306.11
83IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
84IL_60643.11
85IL_40845.11
86IL_92280.11
87IL_57977.11
88IL_02835.11
89IL_25307.11
90IL_66744.11SSU Helix 21 (h21) IL2 E.coli
91IL_06808.11Double sheared (tSH-tSH) one bulged base.
92IL_03931.1116S h19 IL and 23S H41 IL
93IL_78809.11
94IL_13682.11
95IL_83856.11
96IL_05221.11
97IL_06471.11
98IL_91904.11
99IL_15205.11
100IL_91044.11
101IL_27668.11
102IL_85805.11
103IL_76263.11
104IL_91379.11
105IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
106IL_55649.11
107IL_54576.11
108IL_81398.11
109IL_53323.11
110IL_26971.11
111IL_02957.11
112IL_85510.11
113IL_06847.11Group II Intron IL
114IL_63952.11
115IL_83250.1116S h40 3WJ T.th.
116IL_03110.11
117IL_68827.11Reverse Kink-Turn
118IL_83920.11
119IL_06468.1116S h40 3WJ E.c.
120IL_05462.11
121IL_97073.11
122IL_02690.11
123IL_75415.11Pseudo-knot forming internal loop
124IL_82113.11
125IL_98924.11
126IL_59529.11
127IL_17603.11
128IL_88367.11
129IL_60649.11Kink-turn
130IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
131IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
132IL_47687.11
133IL_31006.11tSH-tHW-L-bif-cWW
134IL_80652.11
135IL_12486.11
136IL_03741.11
137IL_25082.11
138IL_71685.11Sarcin-like with an intercalated basepair
139IL_25181.11
140IL_56513.11
141IL_40527.11Kink-turn
142IL_77296.11
143IL_39324.11
144IL_89794.11
145IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
146IL_37715.11
147IL_54450.11
148IL_77014.11
149IL_91078.11
150IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
151IL_23639.11tWH-tHS-L-cWW
152IL_21421.11
153IL_41139.11
154IL_03282.11
155IL_88865.11
156IL_86059.11
157IL_12507.11
158IL_53988.11
159IL_52509.11
160IL_71942.11
161IL_67735.11
162IL_76486.11Sarcin-ricin motif with syn G
163IL_37990.11
164IL_58454.11
165IL_91089.11
166IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
167IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
168IL_41791.11
169IL_43316.11
170IL_80505.11
171IL_26868.11
172IL_11778.11
173IL_27243.11
174IL_75328.11
175IL_97842.11
176IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
177IL_82601.11Tandem cWW water-inserted CU pairs
178IL_23448.11
179IL_57285.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.62391-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.6201cWW AG or water inserted cWW Y-Y.
3IL_39199.354Hoogsteen-edge Platform, Single bulged base
4IL_41766.349Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.343Sugar-edge, 1-base platform, consensus tHS
7IL_87904.431Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.326cWH basepair with syn base
9IL_13959.324Double Sheared (tSH-tHS)
10IL_65553.522Kink-turn
11IL_93424.322tSH-inserted-tHW
12IL_73276.220C-loop
13IL_55938.318LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.31716S h21 S8 binding site
15IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_94430.41516S h32-h33-h34 3WJ
18IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19IL_46648.21123S H91 IL | Single-Base Intercalation Site
20IL_40090.31116S h34 ILa : Part of larger motif
21IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_90459.39cWW AG or UU
24IL_58291.39Recurrent Sub-motif found in junctions
25IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
27IL_25230.36Bacterial 5S rRNA Loop E
28IL_90133.26
29IL_97057.36
30IL_53635.36LSU Helix 32 (H32) IL
31IL_13069.36LSU 3WJ H32-H33-H35A
32IL_72158.36LSU Helix 62 (H62) IL
33IL_79083.35
34IL_08926.2523S H91 IL
35IL_45262.35
36IL_86357.35LSU Helix 61 IL2
37IL_02359.35
38IL_38807.34
39IL_34363.24Kink-turn from 23S H42
40IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
41IL_21333.24tSH-tHW-bulge
42IL_16166.3423S H91 IL
43IL_98591.34
44IL_89028.53Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
45IL_48918.23Kink-turn variant
46IL_34156.63cWW AG or UU
47IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
48IL_98421.33SSU Helix 12 (h12) IL
49IL_62499.63
50IL_23262.42
51IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW

Removed motif groups

#Motif idInstancesDescription
1IL_91487.12116S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_06429.315cWW-bulge-cWW
3IL_27618.21123S H73 ILa : Part of larger Motif
4IL_10007.27Single sheared with bulged bases
5IL_38960.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
6IL_01239.15
7IL_98556.44
8IL_87218.1423S H91 IL
9IL_40387.44LSU Helix 89 (H89) IL2
10IL_53774.13Single sheared with bulged bases
11IL_36254.13
12IL_57216.13tHS tHH bulge with S-turn
13IL_25174.12
14IL_91132.12
15IL_79870.12tHS tHH bulge with S-turn
16IL_06635.12
17IL_81441.12
18IL_16377.12
19IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
20IL_41397.22LSU Helix 96 (H96) IL2
21IL_64648.12tHS tHH bulge with S-turn
22IL_42397.12
23IL_03914.11
24IL_44803.11
25IL_77195.11
26IL_31241.11
27IL_55934.11kink-turn-like
28IL_82519.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
29IL_98688.11
30IL_11869.11
31IL_61991.11
32IL_63837.11tHS tHH bulge with S-turn
33IL_18755.11
34IL_88403.11
35IL_22579.11
36IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
37IL_90880.11

Added motif groups

#Motif idInstancesDescription
1IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
4IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
5IL_16207.15Single sheared with bulged bases
6IL_08559.14LSU Helix 89 (H89) IL2
7IL_01080.14
8IL_42251.14
9IL_80348.1323S H91 IL
10IL_10647.13tHS tHH bulge with S-turn
11IL_56077.13
12IL_92267.1323S H73 ILa : Part of larger Motif
13IL_69536.12LSU Helix 96 (H96) IL2
14IL_19898.12
15IL_33925.12
16IL_09587.12
17IL_24358.12
18IL_33964.12
19IL_88180.12cWW-bulge-cWW
20IL_09901.12tHS tHH bulge with S-turn
21IL_49550.12tHS tHH bulge with S-turn
22IL_91273.12
23IL_04550.11tHS tHH bulge with S-turn
24IL_30354.11
25IL_42891.11
26IL_31290.11
27IL_09491.11
28IL_21221.11SSU Helix 12 (h12) IL
29IL_46721.11
30IL_87394.11
31IL_47732.11
32IL_28468.11Single sheared with bulged bases
33IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
34IL_28644.11
35IL_52610.11
36IL_13434.11
37IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
38IL_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.
39IL_30067.11
40IL_64589.11
41IL_95774.11tHS tHH bulge with S-turn