Changes in PDB files used for clustering

Release 1.0 has 199 PDB files, release 1.1 has 199 PDB files, 197 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_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
3IL_47444.39SRP Loop E-like motif
4IL_92114.39GAAA loop receptor "platform" motif
5IL_73000.27cHS-cWS
6IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
7IL_70237.36
8IL_54420.16
9IL_78732.35Double S-turn motif
10IL_92484.15
11IL_82188.15LSU H68 IL from H.m.
12IL_25300.1516S h19 IL and 23S H41 IL
13IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
14IL_77263.15Kink-turn from U4
15IL_28572.1416S h18 kink-turn like motif
16IL_31066.24SSU Helix 44 (h44) extension
17IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
18IL_71565.24
19IL_22732.14tSH-inserted-tHS
20IL_39526.44
21IL_37053.13Kink-turn from 23S H58
22IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
23IL_05723.13
24IL_30840.13
25IL_75447.13
26IL_79955.23SSU Helix (23) h23 IL1
27IL_82563.13Thi-box riboswitch T-loop
28IL_95150.33
29IL_80494.23LSU H58 IL2 H.m.
30IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
31IL_43946.13
32IL_52173.13
33IL_58586.23
34IL_34628.23Kink-turn
35IL_07300.12
36IL_52940.12
37IL_55287.12
38IL_89231.12LSU H77
39IL_97833.12
40IL_28942.12
41IL_37197.12
42IL_46435.12
43IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
44IL_09882.12
45IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
46IL_40892.12
47IL_70280.12Double sheared with wobble cWW.
48IL_90057.12
49IL_94744.12Sarcin-ricin motif with extra cWW GA pair
50IL_98566.12
51IL_15840.22Triple Sheared with unpaired, inserted A
52IL_37406.12
53IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
54IL_76095.32Motif from Hairpin Ribozyme
55IL_11751.12
56IL_16252.3223S H91 IL
57IL_21495.12
58IL_80093.12
59IL_16330.12
60IL_31707.12Vitamin B12 aptamer
61IL_50521.12
62IL_65137.12Kink-turn like motif in Group I Intron
63IL_77076.12
64IL_00998.12
65IL_12211.12
66IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
67IL_23414.12
68IL_87548.12
69IL_01054.12
70IL_27892.12
71IL_45794.12
72IL_02690.11
73IL_05221.11
74IL_12507.11
75IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
76IL_25082.11
77IL_40527.11Kink-turn
78IL_46306.11
79IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
80IL_67735.11
81IL_81398.11
82IL_83856.11
83IL_92280.11
84IL_05462.11
85IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
86IL_13682.11
87IL_20775.11tSH-inserted
88IL_25181.11
89IL_40845.11
90IL_52958.11
91IL_55649.11
92IL_60643.11
93IL_75415.11Pseudo-knot forming internal loop
94IL_82113.11
95IL_83920.11
96IL_89794.11
97IL_97842.11
98IL_02835.11
99IL_15205.11
100IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
101IL_37347.11
102IL_53323.11
103IL_56513.11
104IL_60649.11Kink-turn
105IL_78809.11
106IL_85510.11
107IL_02957.11
108IL_06306.11
109IL_11302.11
110IL_21421.11
111IL_41139.11
112IL_47687.11
113IL_53988.11
114IL_61730.11
115IL_85805.11
116IL_91044.11
117IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
118IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
119IL_03110.11
120IL_06468.1116S h40 3WJ E.c.
121IL_25307.11
122IL_37715.11
123IL_41791.11
124IL_57977.11
125IL_63952.11
126IL_76486.11Sarcin-ricin motif with syn G
127IL_82601.11Tandem cWW water-inserted CU pairs
128IL_86059.11
129IL_91078.11
130IL_98924.11
131IL_03282.11
132IL_06471.11
133IL_11778.11
134IL_26868.11
135IL_37990.11
136IL_43316.11
137IL_54450.11
138IL_58454.11
139IL_71685.11Sarcin-like with an intercalated basepair
140IL_82650.11
141IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
142IL_91089.11
143IL_03741.11
144IL_06808.11Double sheared (tSH-tSH) one bulged base.
145IL_26971.11
146IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
147IL_39324.11
148IL_54576.11
149IL_65788.11
150IL_71942.11
151IL_80505.11
152IL_83250.1116S h40 3WJ T.th.
153IL_91904.11
154IL_97073.11
155IL_03931.1116S h19 IL and 23S H41 IL
156IL_06847.11Group II Intron IL
157IL_12486.11
158IL_17603.11
159IL_23639.11tWH-tHS-L-cWW
160IL_52509.11
161IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
162IL_59529.11
163IL_66744.11SSU Helix 21 (h21) IL2 E.coli
164IL_77296.11
165IL_80652.11
166IL_88367.11
167IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.

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_93424.322tSH-inserted-tHW
11IL_65553.522Kink-turn
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_40090.31116S h34 ILa : Part of larger motif
20IL_46648.21123S H91 IL | Single-Base Intercalation Site
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_58291.39Recurrent Sub-motif found in junctions
24IL_90459.39cWW AG or UU
25IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26IL_53635.36LSU Helix 32 (H32) IL
27IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
28IL_13069.36LSU 3WJ H32-H33-H35A
29IL_25230.36Bacterial 5S rRNA Loop E
30IL_97057.36
31IL_90133.26
32IL_72158.36LSU Helix 62 (H62) IL
33IL_08926.2523S H91 IL
34IL_79083.35
35IL_86357.35LSU Helix 61 IL2
36IL_45262.35
37IL_02359.35
38IL_98591.34
39IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
40IL_16166.3423S H91 IL
41IL_34363.24Kink-turn from 23S H42
42IL_38807.34
43IL_21333.24tSH-tHW-bulge
44IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
45IL_34156.63cWW AG or UU
46IL_62499.63
47IL_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.
48IL_48918.23Kink-turn variant
49IL_98421.33SSU Helix 12 (h12) IL
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_79870.12tHS tHH bulge with S-turn
14IL_06635.12
15IL_81441.12
16IL_16377.12
17IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
18IL_41397.22LSU Helix 96 (H96) IL2
19IL_64648.12tHS tHH bulge with S-turn
20IL_42397.12
21IL_25174.12
22IL_91132.12
23IL_31241.11
24IL_55934.11kink-turn-like
25IL_82519.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
26IL_98688.11
27IL_11869.11
28IL_61991.11
29IL_63837.11tHS tHH bulge with S-turn
30IL_18755.11
31IL_88403.11
32IL_22579.11
33IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
34IL_90880.11
35IL_03914.11
36IL_44803.11
37IL_77195.11

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_92267.1323S H73 ILa : Part of larger Motif
10IL_10647.13tHS tHH bulge with S-turn
11IL_56077.13
12IL_80348.1323S H91 IL
13IL_19898.12
14IL_88180.12cWW-bulge-cWW
15IL_33925.12
16IL_91273.12
17IL_09587.12
18IL_24358.12
19IL_33964.12
20IL_49550.12tHS tHH bulge with S-turn
21IL_09901.12tHS tHH bulge with S-turn
22IL_69536.12LSU Helix 96 (H96) IL2
23IL_31290.11
24IL_46721.11
25IL_09491.11
26IL_21221.11SSU Helix 12 (h12) IL
27IL_47732.11
28IL_28468.11Single sheared with bulged bases
29IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
30IL_52610.11
31IL_28644.11
32IL_95774.11tHS tHH bulge with S-turn
33IL_13434.11
34IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
35IL_64589.11
36IL_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.
37IL_30067.11
38IL_04550.11tHS tHH bulge with S-turn
39IL_30354.11