Changes in PDB files used for clustering

Release 1.0 has 206 PDB files, release 1.1 has 208 PDB files, 204 of them are identical.

1 equivalence classes changed representatives: 2ZJR4IOA.

3 new structures in release 1.1: 3ZP8, 4ILL, 4ILM.

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 252 motif groups, release 1.1 has 254 motif groups, 190 of them are identical.

40 motif groups were updated, 22 groups are present only in release 1.0, 24 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
1HL_74465.212tRNA Anti-Codon loop
2HL_48039.111MS2 virus RNA Hairpin
3HL_46175.11016S helix 23 and 24 hairpin loops
4HL_15603.18U1A protein-binding Hairpin Loop.
5HL_82294.28SSU Helix 37 (h37) Hairpin loop.
6HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
7HL_42677.16
8HL_72273.15tRNA D-loop
9HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
10HL_45018.35Hairpin-Hairpin Interacting HL
11HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
12HL_06643.25tRNA D-loop. Sec tRNA
13HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
14HL_29831.14GNRA-like with bulged base.
15HL_64543.14SSU Helix 31 (h31) Hairpin Loop
16HL_62881.14RNase P Structured Hairpin Loop
17HL_47784.14SSU Central Pseudoknot (forms helix 2)
18HL_98523.14GNRA-like. Closed by tSH UC.
19HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
20HL_13707.23cSH AA Platform containing Hairpin Loop
21HL_58083.23
22HL_25124.13tSW GA closed tetraloops
23HL_54751.13
24HL_42687.23
25HL_46794.23
26HL_98833.13
27HL_42077.23LSU Helix 28 (H28) Hairpin Loop
28HL_41827.13
29HL_23182.13
30HL_32644.13LSU Helix 69 (H69) Hairpin Loop
31HL_78361.13
32HL_08382.23
33HL_19221.23
34HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
35HL_74686.13SSU Central Pseudoknot (forms helix 2)
36HL_80492.23tRNA D-loop
37HL_24711.12
38HL_12595.12
39HL_24473.32tRNA D-loop
40HL_77555.12
41HL_33451.12
42HL_98577.12
43HL_03791.12
44HL_99633.12
45HL_68697.12
46HL_06122.12
47HL_57904.12
48HL_38130.22
49HL_57014.12
50HL_84353.12
51HL_75575.12
52HL_94578.12
53HL_16770.12
54HL_06312.12
55HL_67692.12
56HL_64371.22
57HL_05361.12
58HL_19399.12
59HL_67367.12
60HL_53753.12
61HL_87554.12
62HL_81752.12
63HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
64HL_49210.12
65HL_76766.12
66HL_62967.12
67HL_65924.12
68HL_23290.12
69HL_42553.12
70HL_26057.12
71HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
72HL_96915.12
73HL_33524.11tRNA T-loop distorted by RS binding
74HL_24707.11
75HL_97499.11
76HL_35004.11
77HL_68435.11
78HL_19132.11
79HL_44390.11
80HL_63304.11
81HL_68733.11LSU Yeast Hairpin Loop
82HL_66900.11
83HL_59610.11
84HL_55543.11
85HL_65802.11
86HL_25197.11
87HL_48480.11
88HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
89HL_37962.11
90HL_58223.11
91HL_58601.11
92HL_88960.11
93HL_56809.11
94HL_00090.11
95HL_55272.11
96HL_47337.11
97HL_90102.11Kink-turn-like Hairpin Loop
98HL_71607.11
99HL_10116.11Kink-turn-like Hairpin Loop
100HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
101HL_30128.11
102HL_59604.11
103HL_57217.11cHS platform Intercalation Site
104HL_20914.11
105HL_26579.11
106HL_66877.11cSH GU/cWS double platform, intercalation site
107HL_27819.11
108HL_67761.11
109HL_53015.11
110HL_78420.11
111HL_95716.11
112HL_82243.11
113HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
114HL_33640.11
115HL_93567.11
116HL_45411.11
117HL_19226.11
118HL_44522.11
119HL_27397.11
120HL_12706.11
121HL_13786.11
122HL_13105.11
123HL_25175.11
124HL_97971.11
125HL_69403.11GNRA-like
126HL_17537.11
127HL_17468.11
128HL_35865.11
129HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
130HL_20806.11
131HL_39422.11
132HL_84289.11
133HL_34440.11
134HL_70912.11
135HL_62970.11
136HL_80746.11
137HL_78228.11
138HL_35200.11
139HL_82288.11
140HL_85018.11
141HL_55202.11U2B"-U2A" binding hairpin loop
142HL_38138.11
143HL_12984.11
144HL_07315.11
145HL_25195.11
146HL_60203.11
147HL_65071.11
148HL_68579.11
149HL_62880.11
150HL_04194.11
151HL_75850.11
152HL_39486.11
153HL_36842.11
154HL_19452.11tRNA D-loop
155HL_81661.11tRNA D-loop
156HL_53789.11
157HL_78507.11
158HL_87223.11
159HL_42969.11
160HL_79902.11
161HL_29084.11
162HL_85753.11
163HL_96192.11
164HL_33277.11
165HL_99207.11Tetrahymena LSU hairpin poorly modeled
166HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
167HL_56775.11
168HL_52393.11Double tSH (double sheared) with bulged base
169HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
170HL_63690.11
171HL_84888.11T-loop like but without tWH UA
172HL_57843.11
173HL_67000.11
174HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
175HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
176HL_66467.11
177HL_97784.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.5224GNRA Hairpin motifs
2HL_72498.663T-loops with two bulged bases
3HL_39895.434UNCG Hairpin motifs
4HL_18781.220Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_97270.215T-loops with 1 bulged base
8HL_49036.211GNRA with one bulged base
9HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
10HL_56824.210LSU Helix 60A. LSU Helix 63A.
11HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_80459.210
13HL_68081.310LSU Helix 20 Hairpin loop
14HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_28436.39LSU Helix 96 (H96) Hairpin Loop
16HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
17HL_34027.285S Loop C - Upper part of Hairpin Loop.
18HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_70420.26LSU Helix 97 Hairpin loop
20HL_87136.26LSU Helix 39A Hairpin loop
21HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
22HL_18156.26LSU Helix 72 (H72) Hairpin Loop
23HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
24HL_75579.26
25HL_39942.26LSU Helix 91 (H91) Hairpin Loop
26HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
27HL_41833.26LSU Helix 81 (H81) Hairpin Loop
28HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
29HL_46489.26LSU H89 Hairpin Loop
30HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
31HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
32HL_88311.25LSU Helix 35 (H35) Hairpin Loop
33HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
34HL_61547.34
35HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
36HL_90579.23
37HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
38HL_76036.33LSU Helix 8 (H8) Hairpin Loop
39HL_27429.33
40HL_82253.23

Removed motif groups

#Motif idInstancesDescription
1HL_95423.25UNCG-like. cWW Closing pair.
2HL_73023.13Two base, cross-stacked hairpin loop
3HL_05510.12
4HL_05797.12
5HL_63823.12
6HL_22614.12
7HL_76105.12
8HL_81555.12
9HL_49267.12
10HL_03431.11
11HL_58786.11
12HL_85138.11LSU Helix 8 (H8) Hairpin Loop
13HL_61061.11
14HL_90365.115S rRNA Loop C from D.radiodurans
15HL_63411.11
16HL_93206.11
17HL_15771.11
18HL_18011.11
19HL_00238.11
20HL_23522.11
21HL_02479.11
22HL_81780.11

Added motif groups

#Motif idInstancesDescription
1HL_57514.15Two base, cross-stacked hairpin loop
2HL_18798.14UNCG-like. cWW Closing pair.
3HL_50312.12
4HL_97512.12LSU Helix 8 (H8) Hairpin Loop
5HL_26495.12
6HL_58687.12
7HL_60200.12
8HL_45440.12
9HL_16118.11
10HL_95049.11Two base, cross-stacked hairpin loop
11HL_52109.11
12HL_96994.11
13HL_24108.11
14HL_30008.11
15HL_31969.11
16HL_73465.11
17HL_01418.11
18HL_42345.11
19HL_81295.11UNCG-like. cWW Closing pair.
20HL_07915.11
21HL_93530.11