Changes in PDB files used for clustering

Release 0.7 has 207 PDB files, release 0.8 has 208 PDB files, 207 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 0.8: 4ATO.

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

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Changes in motif groups

Release 0.7 has 246 motif groups, release 0.8 has 246 motif groups, 245 of them are identical.

1 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.

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_67042.3222GNRA Hairpin motifs
2HL_72498.462T-loops with two bulged bases
3HL_39895.334UNCG Hairpin motifs
4HL_18781.121Double sheared (tSH) with U-turn
5HL_91226.217Kissing Hairpin motif
6HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_97270.115T-loops with 1 bulged base
8HL_74465.111tRNA Anti-Codon loop
9HL_80459.111
10HL_48039.111MS2 virus RNA Hairpin
11HL_46175.11016S helix 23 and 24 hairpin loops
12HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
13HL_49036.110GNRA with one bulged base
14HL_56824.110LSU Helix 60A. LSU Helix 63A.
15HL_68081.210LSU Helix 20 Hairpin loop
16HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_28436.29LSU Helix 96 (H96) Hairpin Loop
18HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
19HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_15603.18U1A protein-binding Hairpin Loop.
21HL_82294.28SSU Helix 37 (h37) Hairpin loop.
22HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_34027.175S Loop C - Upper part of Hairpin Loop.
24HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
26HL_46489.16LSU H89 Hairpin Loop
27HL_39942.16LSU Helix 91 (H91) Hairpin Loop
28HL_70420.16LSU Helix 97 Hairpin loop
29HL_42677.16
30HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
31HL_18156.16LSU Helix 72 (H72) Hairpin Loop
32HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
33HL_75579.16
34HL_87136.16LSU Helix 39A Hairpin loop
35HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
36HL_41833.16LSU Helix 81 (H81) Hairpin Loop
37HL_72273.15tRNA D-loop
38HL_19261.15SSU Central Pseudoknot (forms helix 2)
39HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
40HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
42HL_88311.15LSU Helix 35 (H35) Hairpin Loop
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_06643.15tRNA D-loop. Sec tRNA
46HL_95423.14UNCG-like. cWW Closing pair.
47HL_98523.14GNRA-like. Closed by tSH UC.
48HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
49HL_64543.14SSU Helix 31 (h31) Hairpin Loop
50HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
51HL_62881.14RNase P Structured Hairpin Loop
52HL_29831.14GNRA-like with bulged base.
53HL_20739.13
54HL_23182.13
55HL_76036.13LSU Helix 8 (H8) Hairpin Loop
56HL_90579.13
57HL_80492.23tRNA D-loop
58HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
59HL_46794.23
60HL_27429.23
61HL_54751.13
62HL_13707.23cSH AA Platform containing Hairpin Loop
63HL_53664.13Double tSH (double sheared) with bulged base
64HL_25124.13tSW GA closed tetraloops
65HL_42687.23
66HL_19221.23
67HL_41827.13
68HL_98833.13
69HL_32644.13LSU Helix 69 (H69) Hairpin Loop
70HL_78361.13
71HL_61547.23
72HL_58083.23
73HL_82253.13
74HL_64371.13
75HL_73023.13Two base, cross-stacked hairpin loop
76HL_08382.23
77HL_42077.23LSU Helix 28 (H28) Hairpin Loop
78HL_75575.12
79HL_87554.12
80HL_24711.12
81HL_49267.12
82HL_98577.12
83HL_70459.12
84HL_81752.12
85HL_49210.12
86HL_19905.12
87HL_77555.12
88HL_42553.12
89HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
90HL_99633.12
91HL_96915.12
92HL_23290.12
93HL_81555.12
94HL_06312.12
95HL_03791.12
96HL_68697.12
97HL_53753.12
98HL_12595.12
99HL_24473.32tRNA D-loop
100HL_94578.12
101HL_33451.12
102HL_22614.12
103HL_57014.12
104HL_05510.12
105HL_44467.12
106HL_06122.12
107HL_57904.12
108HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
109HL_46981.12
110HL_14013.12
111HL_05797.12
112HL_84353.12
113HL_65924.12
114HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
115HL_19399.12
116HL_76105.12
117HL_76766.12
118HL_63823.12
119HL_16770.12
120HL_38130.22
121HL_05361.12
122HL_93015.12
123HL_67692.12
124HL_26057.12
125HL_38898.11
126HL_56775.11
127HL_33640.11
128HL_65802.11
129HL_35865.11
130HL_25197.11
131HL_58786.11
132HL_25195.11
133HL_87223.11
134HL_00721.11
135HL_63411.11
136HL_45358.11Double hairpin loop based on GGA triple
137HL_84888.11T-loop like but without tWH UA
138HL_19132.11
139HL_91613.11
140HL_62970.11
141HL_01987.11
142HL_75850.11
143HL_39486.11
144HL_82288.11
145HL_85018.11
146HL_17008.11Nova-2 KH3 domain binding hairpin
147HL_59610.11
148HL_23522.11
149HL_27831.11
150HL_59604.11
151HL_97499.11
152HL_63690.11
153HL_65071.11
154HL_68435.11
155HL_88960.11
156HL_85753.11
157HL_62880.11
158HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
159HL_33277.11
160HL_36842.11
161HL_19452.11tRNA D-loop
162HL_55543.11
163HL_81661.11tRNA D-loop
164HL_37962.11
165HL_02479.11
166HL_61061.11
167HL_58223.11
168HL_58601.11
169HL_66877.11cSH GU/cWS double platform, intercalation site
170HL_67000.11
171HL_96192.11
172HL_66467.11
173HL_99207.11Tetrahymena LSU hairpin poorly modeled
174HL_98233.11
175HL_17468.11
176HL_30128.11
177HL_48480.11
178HL_57217.11cHS platform Intercalation Site
179HL_35004.11
180HL_03431.11
181HL_00238.11
182HL_26579.11
183HL_66880.11
184HL_44390.11
185HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
186HL_47337.11
187HL_68733.11LSU Yeast Hairpin Loop
188HL_97784.11
189HL_33524.11tRNA T-loop distorted by RS binding
190HL_93567.11
191HL_20806.11
192HL_93206.11
193HL_44522.11
194HL_84289.11
195HL_27397.11
196HL_56809.11
197HL_63304.11
198HL_78420.11
199HL_90102.11Kink-turn-like Hairpin Loop
200HL_18011.11
201HL_66900.11
202HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
203HL_99779.11
204HL_81780.11
205HL_90365.115S rRNA Loop C from D.radiodurans
206HL_39422.11
207HL_34440.11
208HL_27819.11
209HL_00090.11
210HL_55272.11
211HL_25175.11
212HL_95716.11
213HL_71607.11
214HL_10116.11Kink-turn-like Hairpin Loop
215HL_55202.11U2B"-U2A" binding hairpin loop
216HL_38138.11
217HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
218HL_07315.11
219HL_45411.11
220HL_78507.11
221HL_20914.11
222HL_05113.11
223HL_79902.11
224HL_30731.11
225HL_12706.11
226HL_67761.11
227HL_53015.11
228HL_97971.11
229HL_82243.11
230HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
231HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
232HL_24707.11
233HL_53789.11
234HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
235HL_15771.11
236HL_42969.11
237HL_57843.11
238HL_68579.11
239HL_70912.11
240HL_13786.11
241HL_04194.11
242HL_78228.11
243HL_35200.11
244HL_69403.11GNRA-like
245HL_17537.11

Updated motif groups

#Motif idInstancesDescription
1HL_45018.35Hairpin-Hairpin Interacting HL

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription