Changes in PDB files used for clustering

Release 0.6 has 185 PDB files, release 0.7 has 191 PDB files, 180 of them are identical.

1 equivalence classes changed representatives: 3UXR3V2F.

10 new structures in release 0.7: 3SYW, 3SZX, 3TZR, 3U4M, 3V7E, 4AOB, 4E48, 4E5C, 4ERD, 4EYA.

Obsolete: 3UXR4V8A.

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 0.6 has 260 motif groups, release 0.7 has 263 motif groups, 142 of them are identical.

59 motif groups were updated, 59 groups are present only in release 0.6, 62 groups are only in release 0.7.

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_92484.15
2IL_01239.15
3IL_82188.15LSU H68 IL from H.m.
4IL_28572.1416S h18 kink-turn like motif
5IL_22732.14tSH-inserted-tHS
6IL_31066.24SSU Helix 44 (h44) extension
7IL_98421.13
8IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
9IL_34363.13Kink-turn from 23S H42
10IL_95150.23
11IL_37053.13Kink-turn from 23S H58
12IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
13IL_15840.13
14IL_52173.13
15IL_30840.13
16IL_62499.23
17IL_79955.23SSU Helix (23) h23 IL1
18IL_82563.13Thi-box riboswitch T-loop
19IL_45794.12
20IL_52940.12
21IL_12211.12
22IL_94744.12Sarcin-ricin motif with extra cWW GA pair
23IL_98566.12
24IL_25174.12
25IL_46435.12
26IL_90057.12
27IL_28942.12
28IL_40892.12
29IL_81441.12
30IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
31IL_37197.12
32IL_50521.12
33IL_70280.12Double sheared with wobble cWW.
34IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
35IL_16166.12
36IL_23414.12
37IL_87173.12
38IL_97833.12
39IL_09882.12
40IL_16330.12
41IL_55287.12
42IL_74876.12
43IL_80093.12
44IL_92459.12
45IL_05221.11
46IL_11302.11
47IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
48IL_24143.11Yeast 18S
49IL_26868.11
50IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
51IL_39324.11
52IL_55649.11
53IL_65788.11
54IL_75415.11Pseudo-knot forming internal loop
55IL_80505.11
56IL_83250.1116S h40 3WJ T.th.
57IL_88403.11
58IL_05462.11
59IL_20775.11tSH-inserted
60IL_25082.11
61IL_26971.11
62IL_32080.11
63IL_40527.11Kink-turn
64IL_46306.11
65IL_52958.11
66IL_55934.11kink-turn-like
67IL_66744.11SSU Helix 21 (h21) IL2 E.coli
68IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
69IL_80652.11
70IL_83920.11
71IL_06306.11
72IL_12233.11
73IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
74IL_40845.11
75IL_53323.11
76IL_59529.11
77IL_67735.11
78IL_76263.11
79IL_81398.11
80IL_85510.11
81IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
82IL_02690.11
83IL_06468.1116S h40 3WJ E.c.
84IL_12486.11
85IL_22579.11
86IL_25181.11
87IL_47687.11
88IL_53988.11
89IL_61723.11
90IL_68827.11Reverse Kink-Turn
91IL_76486.11Sarcin-ricin motif with syn G
92IL_85805.11
93IL_91078.11
94IL_98924.11
95IL_02835.11
96IL_06808.11Double sheared (tSH-tSH) one bulged base.
97IL_15205.11
98IL_29949.11
99IL_41009.11
100IL_54450.11
101IL_61730.11
102IL_82113.11
103IL_86059.11
104IL_91089.11
105IL_96260.11
106IL_02957.11
107IL_07375.11
108IL_22858.11
109IL_25307.11
110IL_30390.11
111IL_37347.11
112IL_41139.11
113IL_54576.11
114IL_62352.11
115IL_71685.11Sarcin-like with an intercalated basepair
116IL_78809.11
117IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
118IL_91904.11
119IL_97073.11
120IL_03110.11
121IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
122IL_25739.11M-Box Riboswitch
123IL_37715.11
124IL_41791.11
125IL_52509.11
126IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
127IL_71942.11
128IL_92280.11
129IL_03741.11
130IL_23639.11tWH-tHS-L-cWW
131IL_26241.11
132IL_37990.11
133IL_43316.11
134IL_52752.11
135IL_63952.11
136IL_82650.11
137IL_88367.11
138IL_97842.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.2234
2IL_47174.220016S h34 ILa : Part of larger motif
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.231Triple sheared
8IL_13959.224Double Sheared (tSH-tHS)
9IL_93424.222tSH-inserted-tHW
10IL_65553.221Kink-turn
11IL_32390.22116S h19 IL and 23S H41 IL
12IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.21716S h21 S8 binding site
14IL_85647.216Sarcin-ricin parent motif with 15 Nts
15IL_31555.21516S decoding site
16IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_94430.21416S h32-h33-h34 3WJ
18IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19IL_40090.21116S h34 ILa : Part of larger motif
20IL_27618.21123S H73 ILa : Part of larger Motif
21IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_58291.29Recurrent Sub-motif found in junctions
23IL_47444.29SRP Loop E-like motif
24IL_92114.29GAAA loop receptor "platform" motif
25IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26IL_90459.28cWW AG or UU
27IL_86357.27LSU Helix 61 IL2
28IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
29IL_73000.27cHS-cWS
30IL_97057.26
31IL_70237.36
32IL_53635.26LSU Helix 32 (H32) IL
33IL_72158.26LSU Helix 62 (H62) IL
34IL_13069.26LSU 3WJ H32-H33-H35A
35IL_24022.26
36IL_25230.26Bacterial 5S rRNA Loop E
37IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
38IL_45262.25
39IL_79083.25
40IL_78732.35Double S-turn motif
41IL_80179.25
42IL_40387.25
43IL_02359.25
44IL_64184.24
45IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
46IL_98591.24
47IL_39526.24
48IL_38807.24
49IL_80494.23LSU H58 IL2 H.m.
50IL_09348.23
51IL_16252.2323S H91 IL
52IL_34628.23Kink-turn
53IL_58586.23
54IL_34156.23cWW AG or UU
55IL_23262.33
56IL_82831.22Kink-turn from 16S H23
57IL_41397.22LSU Helix 96 (H96) IL2
58IL_76095.32Motif from Hairpin Ribozyme
59IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS

Removed motif groups

#Motif idInstancesDescription
1IL_11616.155cWH basepair with syn base
2IL_54307.127C-loop
3IL_73663.1151 or 2 bulged bases
4IL_48187.111Single sheared with bulged bases
5IL_99515.11123S H91 IL
6IL_68939.19Kink-turn from U4
7IL_40239.18Leadzyme Motif
8IL_76831.18REV element IL with syn G
9IL_82367.47
10IL_29610.16
11IL_24476.15
12IL_78157.15
13IL_92936.15
14IL_93335.25
15IL_59016.15
16IL_18947.14
17IL_69124.14
18IL_11167.34
19IL_49111.14tHS tHH bulge with S-turn
20IL_11594.14
21IL_92333.14
22IL_13740.13
23IL_99434.13Single-Base Intercalation Site
24IL_30979.13
25IL_10804.13
26IL_68736.12
27IL_02691.12
28IL_44742.12
29IL_57870.12
30IL_88684.12
31IL_09390.12
32IL_47247.12
33IL_69009.12
34IL_89461.12
35IL_62718.12
36IL_19202.12
37IL_63741.12
38IL_91543.12
39IL_19889.12
40IL_75449.12
41IL_92123.12
42IL_67117.12
43IL_39230.11
44IL_67697.11
45IL_55167.11
46IL_14225.11
47IL_29877.11
48IL_99165.11
49IL_17109.11
50IL_30650.11
51IL_10109.11H71 junction in 23S rRNA of T.th.
52IL_91513.11
53IL_31793.11Kink-turn from 16S H23
54IL_48650.11
55IL_38333.11
56IL_65978.11
57IL_24335.11
58IL_39165.11
59IL_50767.11

Added motif groups

#Motif idInstancesDescription
1IL_06390.125cWH basepair with syn base
2IL_73276.120C-loop
3IL_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
4IL_46648.11123S H91 IL | Single-Base Intercalation Site
5IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
7IL_08926.1623S H91 IL
8IL_10007.16Single sheared with bulged bases
9IL_89088.1616S h19 IL and 23S H41 IL
10IL_07911.15
11IL_77263.15Kink-turn from U4
12IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
13IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
14IL_98556.14
15IL_21333.14tSH-tHW-bulge
16IL_75447.13
17IL_53774.13Single sheared with bulged bases
18IL_71565.13
19IL_43946.13
20IL_45808.13
21IL_21495.12
22IL_91026.12
23IL_14023.12
24IL_00998.12
25IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
26IL_31707.12Vitamin B12 aptamer
27IL_78674.12tHS tHH bulge with S-turn
28IL_01054.12
29IL_37406.12
30IL_48285.12Leadzyme Motif
31IL_65137.12Kink-turn like motif in Group I Intron
32IL_12068.12
33IL_87548.12
34IL_99575.12
35IL_12269.12
36IL_43933.12
37IL_74291.12
38IL_13942.11
39IL_57977.11
40IL_31241.11
41IL_47457.11
42IL_58454.11
43IL_95939.11
44IL_60643.11
45IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
46IL_11869.11
47IL_17603.11
48IL_82601.11Tandem cWW water-inserted CU pairs
49IL_18755.11
50IL_41849.11
51IL_53423.11
52IL_12507.11
53IL_56513.11
54IL_89794.11
55IL_07675.11tHS tHH bulge with S-turn
56IL_13682.11
57IL_21421.11
58IL_56779.11
59IL_90880.11