Changes in PDB files used for clustering

Release 0.8 has 208 PDB files, release 1.0 has 211 PDB files, 208 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.0: 3W3S, 4B5R, 4HXH.

No equivalence class representatives have been obsoleted.

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 0.8 has 246 motif groups, release 1.0 has 252 motif groups, 227 of them are identical.

9 motif groups were updated, 10 groups are present only in release 0.8, 16 groups are only in release 1.0.

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_39895.334UNCG Hairpin motifs
2HL_18781.121Double sheared (tSH) with U-turn
3HL_91226.217Kissing Hairpin motif
4HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
5HL_97270.115T-loops with 1 bulged base
6HL_80459.111
7HL_48039.111MS2 virus RNA Hairpin
8HL_68081.210LSU Helix 20 Hairpin loop
9HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
10HL_49036.110GNRA with one bulged base
11HL_56824.110LSU Helix 60A. LSU Helix 63A.
12HL_46175.11016S helix 23 and 24 hairpin loops
13HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
14HL_28436.29LSU Helix 96 (H96) Hairpin Loop
15HL_82294.28SSU Helix 37 (h37) Hairpin loop.
16HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
17HL_15603.18U1A protein-binding Hairpin Loop.
18HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
19HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
20HL_34027.175S Loop C - Upper part of Hairpin Loop.
21HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
22HL_46489.16LSU H89 Hairpin Loop
23HL_42677.16
24HL_39942.16LSU Helix 91 (H91) Hairpin Loop
25HL_70420.16LSU Helix 97 Hairpin loop
26HL_18156.16LSU Helix 72 (H72) Hairpin Loop
27HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
29HL_75579.16
30HL_87136.16LSU Helix 39A Hairpin loop
31HL_41833.16LSU Helix 81 (H81) Hairpin Loop
32HL_45018.35Hairpin-Hairpin Interacting HL
33HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
34HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
35HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
36HL_72273.15tRNA D-loop
37HL_88311.15LSU Helix 35 (H35) Hairpin Loop
38HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_62881.14RNase P Structured Hairpin Loop
41HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
42HL_98523.14GNRA-like. Closed by tSH UC.
43HL_29831.14GNRA-like with bulged base.
44HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
45HL_64543.14SSU Helix 31 (h31) Hairpin Loop
46HL_98833.13
47HL_41827.13
48HL_61547.23
49HL_23182.13
50HL_46794.23
51HL_08382.23
52HL_42077.23LSU Helix 28 (H28) Hairpin Loop
53HL_73023.13Two base, cross-stacked hairpin loop
54HL_90579.13
55HL_25124.13tSW GA closed tetraloops
56HL_19221.23
57HL_27429.23
58HL_82253.13
59HL_78361.13
60HL_13707.23cSH AA Platform containing Hairpin Loop
61HL_58083.23
62HL_80492.23tRNA D-loop
63HL_54751.13
64HL_42687.23
65HL_32644.13LSU Helix 69 (H69) Hairpin Loop
66HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
67HL_33451.12
68HL_99633.12
69HL_96915.12
70HL_53753.12
71HL_94578.12
72HL_49267.12
73HL_98577.12
74HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
75HL_68697.12
76HL_81752.12
77HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
78HL_49210.12
79HL_03791.12
80HL_65924.12
81HL_23290.12
82HL_05361.12
83HL_44467.12
84HL_06122.12
85HL_24711.12
86HL_24473.32tRNA D-loop
87HL_57014.12
88HL_05510.12
89HL_63823.12
90HL_84353.12
91HL_12595.12
92HL_06312.12
93HL_05797.12
94HL_16770.12
95HL_57904.12
96HL_38130.22
97HL_42553.12
98HL_22614.12
99HL_76105.12
100HL_76766.12
101HL_75575.12
102HL_19905.12
103HL_77555.12
104HL_81555.12
105HL_19399.12
106HL_67692.12
107HL_26057.12
108HL_87554.12
109HL_38898.11
110HL_65802.11
111HL_35865.11
112HL_30128.11
113HL_48480.11
114HL_78507.11
115HL_87223.11
116HL_00721.11
117HL_63411.11
118HL_45358.11Double hairpin loop based on GGA triple
119HL_84888.11T-loop like but without tWH UA
120HL_19132.11
121HL_91613.11
122HL_85753.11
123HL_62880.11
124HL_66467.11
125HL_99207.11Tetrahymena LSU hairpin poorly modeled
126HL_98233.11
127HL_17008.11Nova-2 KH3 domain binding hairpin
128HL_38138.11
129HL_33640.11
130HL_93567.11
131HL_99779.11
132HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
133HL_63690.11
134HL_65071.11
135HL_68435.11
136HL_88960.11
137HL_67000.11
138HL_96192.11
139HL_47337.11
140HL_68733.11LSU Yeast Hairpin Loop
141HL_97784.11
142HL_23522.11
143HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
144HL_45411.11
145HL_02479.11
146HL_61061.11
147HL_58223.11
148HL_58601.11
149HL_66877.11cSH GU/cWS double platform, intercalation site
150HL_44390.11
151HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
152HL_78420.11
153HL_90102.11Kink-turn-like Hairpin Loop
154HL_18011.11
155HL_66900.11
156HL_33524.11tRNA T-loop distorted by RS binding
157HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
158HL_56775.11
159HL_07315.11
160HL_59604.11
161HL_97499.11
162HL_35004.11
163HL_03431.11
164HL_00238.11
165HL_26579.11
166HL_66880.11
167HL_56809.11
168HL_63304.11
169HL_25175.11
170HL_95716.11
171HL_71607.11
172HL_10116.11Kink-turn-like Hairpin Loop
173HL_81661.11tRNA D-loop
174HL_17468.11
175HL_53789.11
176HL_25195.11
177HL_37962.11
178HL_93206.11
179HL_44522.11
180HL_84289.11
181HL_27397.11
182HL_27819.11
183HL_00090.11
184HL_55272.11
185HL_97971.11
186HL_82243.11
187HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
188HL_59610.11
189HL_55543.11
190HL_24707.11
191HL_58786.11
192HL_57217.11cHS platform Intercalation Site
193HL_81780.11
194HL_90365.115S rRNA Loop C from D.radiodurans
195HL_39422.11
196HL_34440.11
197HL_12706.11
198HL_67761.11
199HL_53015.11
200HL_78228.11
201HL_35200.11
202HL_69403.11GNRA-like
203HL_17537.11
204HL_55202.11U2B"-U2A" binding hairpin loop
205HL_25197.11
206HL_20806.11
207HL_20914.11
208HL_05113.11
209HL_79902.11
210HL_30731.11
211HL_70912.11
212HL_13786.11
213HL_04194.11
214HL_75850.11
215HL_39486.11
216HL_82288.11
217HL_85018.11
218HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
219HL_15771.11
220HL_42969.11
221HL_57843.11
222HL_68579.11
223HL_62970.11
224HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
225HL_33277.11
226HL_36842.11
227HL_19452.11tRNA D-loop

Updated motif groups

#Motif idInstancesDescription
1HL_67042.4225GNRA Hairpin motifs
2HL_72498.563T-loops with two bulged bases
3HL_74465.212tRNA Anti-Codon loop
4HL_17723.210LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
5HL_01926.26LSU Helix 71 (H71) Hairpin Loop.
6HL_95423.25UNCG-like. cWW Closing pair.
7HL_06643.25tRNA D-loop. Sec tRNA
8HL_76036.23LSU Helix 8 (H8) Hairpin Loop
9HL_64371.22

Removed motif groups

#Motif idInstancesDescription
1HL_19261.15SSU Central Pseudoknot (forms helix 2)
2HL_20739.13
3HL_53664.13Double tSH (double sheared) with bulged base
4HL_46981.12
5HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
6HL_70459.12
7HL_14013.12
8HL_93015.12
9HL_27831.11
10HL_01987.11

Added motif groups

#Motif idInstancesDescription
1HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
2HL_47784.14SSU Central Pseudoknot (forms helix 2)
3HL_74686.13SSU Central Pseudoknot (forms helix 2)
4HL_67367.12
5HL_62967.12
6HL_19226.11
7HL_29084.11
8HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
9HL_80746.11
10HL_52393.11Double tSH (double sheared) with bulged base
11HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
12HL_57923.11
13HL_85138.11LSU Helix 8 (H8) Hairpin Loop
14HL_12984.11
15HL_60203.11
16HL_13105.11