Changes in PDB files used for clustering

Release 1.0 has 211 PDB files, release 1.1 has 213 PDB files, 209 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_82294.28SSU Helix 37 (h37) Hairpin loop.
5HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
6HL_15603.18U1A protein-binding Hairpin Loop.
7HL_42677.16
8HL_45018.35Hairpin-Hairpin Interacting HL
9HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
10HL_72273.15tRNA D-loop
11HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
12HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
13HL_06643.25tRNA D-loop. Sec tRNA
14HL_47784.14SSU Central Pseudoknot (forms helix 2)
15HL_98523.14GNRA-like. Closed by tSH UC.
16HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
17HL_29831.14GNRA-like with bulged base.
18HL_64543.14SSU Helix 31 (h31) Hairpin Loop
19HL_62881.14RNase P Structured Hairpin Loop
20HL_98833.13
21HL_42077.23LSU Helix 28 (H28) Hairpin Loop
22HL_41827.13
23HL_23182.13
24HL_08382.23
25HL_19221.23
26HL_74686.13SSU Central Pseudoknot (forms helix 2)
27HL_80492.23tRNA D-loop
28HL_32644.13LSU Helix 69 (H69) Hairpin Loop
29HL_25124.13tSW GA closed tetraloops
30HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
31HL_13707.23cSH AA Platform containing Hairpin Loop
32HL_58083.23
33HL_54751.13
34HL_42687.23
35HL_46794.23
36HL_78361.13
37HL_57014.12
38HL_53753.12
39HL_81752.12
40HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
41HL_49210.12
42HL_05361.12
43HL_06312.12
44HL_67692.12
45HL_98577.12
46HL_87554.12
47HL_65924.12
48HL_23290.12
49HL_19399.12
50HL_67367.12
51HL_24711.12
52HL_12595.12
53HL_24473.32tRNA D-loop
54HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
55HL_62967.12
56HL_06122.12
57HL_57904.12
58HL_38130.22
59HL_77555.12
60HL_42553.12
61HL_64371.22
62HL_03791.12
63HL_96915.12
64HL_84353.12
65HL_75575.12
66HL_33451.12
67HL_76766.12
68HL_44467.12
69HL_99633.12
70HL_68697.12
71HL_16770.12
72HL_94578.12
73HL_26057.12
74HL_38898.11
75HL_17468.11
76HL_35865.11
77HL_93567.11
78HL_57923.11
79HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
80HL_37962.11
81HL_45358.11Double hairpin loop based on GGA triple
82HL_42969.11
83HL_79902.11
84HL_30731.11
85HL_12706.11
86HL_67761.11
87HL_53015.11
88HL_78420.11
89HL_95716.11
90HL_82243.11
91HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
92HL_17008.11Nova-2 KH3 domain binding hairpin
93HL_38138.11
94HL_12984.11
95HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
96HL_45411.11
97HL_59604.11
98HL_57217.11cHS platform Intercalation Site
99HL_20914.11
100HL_68435.11
101HL_84888.11T-loop like but without tWH UA
102HL_57843.11
103HL_68579.11
104HL_70912.11
105HL_13786.11
106HL_13105.11
107HL_25175.11
108HL_97971.11
109HL_69403.11GNRA-like
110HL_17537.11
111HL_81661.11tRNA D-loop
112HL_07315.11
113HL_19226.11
114HL_58223.11
115HL_19132.11
116HL_91613.11
117HL_62970.11
118HL_80746.11
119HL_78228.11
120HL_35200.11
121HL_82288.11
122HL_85018.11
123HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
124HL_56775.11
125HL_52393.11Double tSH (double sheared) with bulged base
126HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
127HL_53789.11
128HL_25195.11
129HL_20806.11
130HL_26579.11
131HL_58601.11
132HL_88960.11
133HL_29084.11
134HL_85753.11
135HL_62880.11
136HL_04194.11
137HL_75850.11
138HL_39486.11
139HL_36842.11
140HL_19452.11tRNA D-loop
141HL_33524.11tRNA T-loop distorted by RS binding
142HL_60203.11
143HL_00721.11
144HL_44522.11
145HL_66877.11cSH GU/cWS double platform, intercalation site
146HL_67000.11
147HL_96192.11
148HL_33277.11
149HL_99207.11Tetrahymena LSU hairpin poorly modeled
150HL_98233.11
151HL_59610.11
152HL_55543.11
153HL_65802.11
154HL_24707.11
155HL_78507.11
156HL_87223.11
157HL_65071.11
158HL_39422.11
159HL_66880.11
160HL_44390.11
161HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
162HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
163HL_66467.11
164HL_97784.11
165HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
166HL_25197.11
167HL_48480.11
168HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
169HL_63690.11
170HL_84289.11
171HL_27397.11
172HL_56809.11
173HL_63304.11
174HL_68733.11LSU Yeast Hairpin Loop
175HL_66900.11
176HL_55202.11U2B"-U2A" binding hairpin loop
177HL_33640.11
178HL_30128.11
179HL_99779.11
180HL_97499.11
181HL_35004.11
182HL_05113.11
183HL_34440.11
184HL_27819.11
185HL_00090.11
186HL_55272.11
187HL_47337.11
188HL_90102.11Kink-turn-like Hairpin Loop
189HL_71607.11
190HL_10116.11Kink-turn-like Hairpin Loop

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_80459.210
10HL_68081.310LSU Helix 20 Hairpin loop
11HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
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_39942.26LSU Helix 91 (H91) Hairpin Loop
20HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
21HL_41833.26LSU Helix 81 (H81) Hairpin Loop
22HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
23HL_46489.26LSU H89 Hairpin Loop
24HL_70420.26LSU Helix 97 Hairpin loop
25HL_87136.26LSU Helix 39A Hairpin loop
26HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
27HL_18156.26LSU Helix 72 (H72) Hairpin Loop
28HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
29HL_75579.26
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_62228.24LSU Helix 35A (H35A) Hairpin Loop
34HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
35HL_61547.34
36HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
37HL_76036.33LSU Helix 8 (H8) Hairpin Loop
38HL_27429.33
39HL_82253.23
40HL_90579.23

Removed motif groups

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

Added motif groups

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