Changes in PDB files used for clustering

Release 1.0 has 207 PDB files, release 1.1 has 209 PDB files, 205 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

Loading the Sankey diagram...

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_45018.35Hairpin-Hairpin Interacting HL
9HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
10HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
11HL_06643.25tRNA D-loop. Sec tRNA
12HL_72273.15tRNA D-loop
13HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
14HL_64543.14SSU Helix 31 (h31) Hairpin Loop
15HL_62881.14RNase P Structured Hairpin Loop
16HL_47784.14SSU Central Pseudoknot (forms helix 2)
17HL_98523.14GNRA-like. Closed by tSH UC.
18HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
19HL_29831.14GNRA-like with bulged base.
20HL_13707.23cSH AA Platform containing Hairpin Loop
21HL_58083.23
22HL_54751.13
23HL_42687.23
24HL_46794.23
25HL_98833.13
26HL_42077.23LSU Helix 28 (H28) Hairpin Loop
27HL_41827.13
28HL_23182.13
29HL_25124.13tSW GA closed tetraloops
30HL_08382.23
31HL_19221.23
32HL_32644.13LSU Helix 69 (H69) Hairpin Loop
33HL_74686.13SSU Central Pseudoknot (forms helix 2)
34HL_80492.23tRNA D-loop
35HL_78361.13
36HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
37HL_84353.12
38HL_75575.12
39HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
40HL_96915.12
41HL_16770.12
42HL_94578.12
43HL_57014.12
44HL_98577.12
45HL_03791.12
46HL_99633.12
47HL_68697.12
48HL_53753.12
49HL_05361.12
50HL_06312.12
51HL_67692.12
52HL_81752.12
53HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
54HL_49210.12
55HL_19399.12
56HL_67367.12
57HL_64371.22
58HL_65924.12
59HL_23290.12
60HL_24711.12
61HL_12595.12
62HL_24473.32tRNA D-loop
63HL_42553.12
64HL_76766.12
65HL_87554.12
66HL_06122.12
67HL_57904.12
68HL_38130.22
69HL_77555.12
70HL_33451.12
71HL_26057.12
72HL_62967.12
73HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
74HL_25197.11
75HL_48480.11
76HL_99779.11
77HL_97499.11
78HL_35004.11
79HL_68435.11
80HL_84888.11T-loop like but without tWH UA
81HL_57843.11
82HL_67000.11
83HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
84HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
85HL_66467.11
86HL_97784.11
87HL_33640.11
88HL_30128.11
89HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
90HL_37962.11
91HL_58223.11
92HL_19132.11
93HL_44390.11
94HL_63304.11
95HL_68733.11LSU Yeast Hairpin Loop
96HL_66900.11
97HL_17468.11
98HL_35865.11
99HL_93567.11
100HL_45411.11
101HL_59604.11
102HL_57217.11cHS platform Intercalation Site
103HL_20914.11
104HL_26579.11
105HL_58601.11
106HL_88960.11
107HL_56809.11
108HL_00090.11
109HL_55272.11
110HL_47337.11
111HL_90102.11Kink-turn-like Hairpin Loop
112HL_71607.11
113HL_10116.11Kink-turn-like Hairpin Loop
114HL_55202.11U2B"-U2A" binding hairpin loop
115HL_38138.11
116HL_12984.11
117HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
118HL_19226.11
119HL_44522.11
120HL_66877.11cSH GU/cWS double platform, intercalation site
121HL_27819.11
122HL_67761.11
123HL_53015.11
124HL_78420.11
125HL_95716.11
126HL_82243.11
127HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
128HL_81661.11tRNA D-loop
129HL_07315.11
130HL_25195.11
131HL_20806.11
132HL_39422.11
133HL_27397.11
134HL_12706.11
135HL_13786.11
136HL_13105.11
137HL_25175.11
138HL_97971.11
139HL_69403.11GNRA-like
140HL_17537.11
141HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
142HL_56775.11
143HL_52393.11Double tSH (double sheared) with bulged base
144HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
145HL_53789.11
146HL_60203.11
147HL_65071.11
148HL_84289.11
149HL_34440.11
150HL_70912.11
151HL_62970.11
152HL_80746.11
153HL_78228.11
154HL_35200.11
155HL_82288.11
156HL_85018.11
157HL_33524.11tRNA T-loop distorted by RS binding
158HL_78507.11
159HL_87223.11
160HL_05113.11
161HL_68579.11
162HL_62880.11
163HL_04194.11
164HL_75850.11
165HL_39486.11
166HL_36842.11
167HL_19452.11tRNA D-loop
168HL_59610.11
169HL_55543.11
170HL_65802.11
171HL_24707.11
172HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
173HL_63690.11
174HL_42969.11
175HL_79902.11
176HL_29084.11
177HL_85753.11
178HL_96192.11
179HL_33277.11
180HL_99207.11Tetrahymena LSU hairpin poorly modeled

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_97270.215T-loops with 1 bulged base
7HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_49036.211GNRA with one bulged base
9HL_56824.210LSU Helix 60A. LSU Helix 63A.
10HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
11HL_80459.210
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_28436.39LSU Helix 96 (H96) Hairpin Loop
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
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_18156.26LSU Helix 72 (H72) Hairpin Loop
20HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
21HL_75579.26
22HL_39942.26LSU Helix 91 (H91) Hairpin Loop
23HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
24HL_41833.26LSU Helix 81 (H81) Hairpin Loop
25HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
26HL_46489.26LSU H89 Hairpin Loop
27HL_70420.26LSU Helix 97 Hairpin loop
28HL_87136.26LSU Helix 39A Hairpin loop
29HL_34108.26LSU Helix 37 (H37) 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_61547.34
34HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
35HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
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_63823.12
4HL_22614.12
5HL_76105.12
6HL_81555.12
7HL_49267.12
8HL_05510.12
9HL_05797.12
10HL_15771.11
11HL_18011.11
12HL_00238.11
13HL_23522.11
14HL_02479.11
15HL_81780.11
16HL_03431.11
17HL_58786.11
18HL_85138.11LSU Helix 8 (H8) Hairpin Loop
19HL_61061.11
20HL_90365.115S rRNA Loop C from D.radiodurans
21HL_63411.11
22HL_93206.11

Added motif groups

#Motif idInstancesDescription
1HL_57514.15Two base, cross-stacked hairpin loop
2HL_18798.14UNCG-like. cWW Closing pair.
3HL_97512.12LSU Helix 8 (H8) Hairpin Loop
4HL_26495.12
5HL_58687.12
6HL_60200.12
7HL_45440.12
8HL_50312.12
9HL_20028.11
10HL_52109.11
11HL_96994.11
12HL_24108.11
13HL_99584.11
14HL_01418.11
15HL_30008.11
16HL_07915.11
17HL_31969.11
18HL_73465.11
19HL_08203.11
20HL_42345.11
21HL_81295.11UNCG-like. cWW Closing pair.
22HL_16118.11
23HL_93530.11
24HL_95049.11Two base, cross-stacked hairpin loop