Changes in PDB files used for clustering

Release 0.4 has 200 PDB files, release 0.5 has 206 PDB files, 200 of them are identical.

No equivalence class representatives have been replaced.

6 new structures in release 0.5: 4AY2, 4FNJ, 4FRG, 4FRN, 4GMA, 4GXY.

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 0.4 has 245 motif groups, release 0.5 has 247 motif groups, 230 of them are identical.

7 motif groups were updated, 8 groups are present only in release 0.4, 10 groups are only in release 0.5.

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_18781.121Double sheared (tSH) with U-turn
2HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
3HL_97270.115T-loops with 1 bulged base
4HL_48039.111MS2 virus RNA Hairpin
5HL_80459.111
6HL_74465.111tRNA Anti-Codon loop
7HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
8HL_49036.110GNRA with one bulged base
9HL_56824.110LSU Helix 60A. LSU Helix 63A.
10HL_46175.11016S helix 23 and 24 hairpin loops
11HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
12HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_15603.18U1A protein-binding Hairpin Loop.
14HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
15HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
16HL_34027.175S Loop C - Upper part of Hairpin Loop.
17HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
19HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
20HL_18156.16LSU Helix 72 (H72) Hairpin Loop
21HL_87136.16LSU Helix 39A Hairpin loop
22HL_41833.16LSU Helix 81 (H81) Hairpin Loop
23HL_42677.16
24HL_75579.16
25HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
26HL_46489.16LSU H89 Hairpin Loop
27HL_39942.16LSU Helix 91 (H91) Hairpin Loop
28HL_70420.16LSU Helix 97 Hairpin loop
29HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_19261.15SSU Central Pseudoknot (forms helix 2)
31HL_06643.15tRNA D-loop. Sec tRNA
32HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
33HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
34HL_72273.15tRNA D-loop
35HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
36HL_88311.15LSU Helix 35 (H35) Hairpin Loop
37HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_64543.14SSU Helix 31 (h31) Hairpin Loop
40HL_62881.14RNase P Structured Hairpin Loop
41HL_98523.14GNRA-like. Closed by tSH UC.
42HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
43HL_08382.14
44HL_29831.14GNRA-like with bulged base.
45HL_45018.24
46HL_95423.14UNCG-like. cWW Closing pair.
47HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
48HL_42687.23
49HL_53664.13Double tSH (double sheared) with bulged base
50HL_58083.23
51HL_82253.13
52HL_73023.13Two base, cross-stacked hairpin loop
53HL_54751.13
54HL_98833.13
55HL_64371.13
56HL_27658.13
57HL_41827.13
58HL_76036.13LSU Helix 8 (H8) Hairpin Loop
59HL_90579.13
60HL_25124.13tSW GA closed tetraloops
61HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
62HL_42077.23LSU Helix 28 (H28) Hairpin Loop
63HL_23182.13
64HL_46794.23
65HL_80492.23tRNA D-loop
66HL_27429.23
67HL_20739.13
68HL_78361.13
69HL_13707.23cSH AA Platform containing Hairpin Loop
70HL_19221.23
71HL_32644.13LSU Helix 69 (H69) Hairpin Loop
72HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
73HL_63823.12
74HL_38130.22
75HL_49267.12
76HL_98577.12
77HL_56859.12
78HL_10832.12
79HL_27809.12
80HL_57904.12
81HL_20857.12
82HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
83HL_61547.12
84HL_87554.12
85HL_65924.12
86HL_49210.12
87HL_42553.12
88HL_57014.12
89HL_05510.12
90HL_70459.12
91HL_99633.12
92HL_96915.12
93HL_06122.12
94HL_23290.12
95HL_19905.12
96HL_33451.12
97HL_05797.12
98HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
99HL_24711.12
100HL_24473.32tRNA D-loop
101HL_88640.12
102HL_14013.12
103HL_76105.12
104HL_76766.12
105HL_03791.12
106HL_16770.12
107HL_94578.12
108HL_19399.12
109HL_67692.12
110HL_26057.12
111HL_44467.12
112HL_38898.11
113HL_17468.11
114HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
115HL_45411.11
116HL_78507.11
117HL_87223.11
118HL_00721.11
119HL_63411.11
120HL_45358.11Double hairpin loop based on GGA triple
121HL_84888.11T-loop like but without tWH UA
122HL_88921.11
123HL_34440.11
124HL_27819.11
125HL_00090.11
126HL_55272.11
127HL_97971.11
128HL_99207.11Tetrahymena LSU hairpin poorly modeled
129HL_17008.11Nova-2 KH3 domain binding hairpin
130HL_20252.11
131HL_07315.11
132HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
133HL_63690.11
134HL_65071.11
135HL_68435.11
136HL_30731.11
137HL_12706.11
138HL_67761.11
139HL_53015.11
140HL_78228.11
141HL_35200.11
142HL_97784.11
143HL_39922.11
144HL_35865.11
145HL_24707.11
146HL_53789.11
147HL_25195.11
148HL_02479.11
149HL_61061.11
150HL_58223.11
151HL_58601.11
152HL_79902.11
153HL_68579.11
154HL_70912.11
155HL_13786.11
156HL_04194.11
157HL_75850.11
158HL_39486.11
159HL_66900.11
160HL_38138.11
161HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
162HL_65802.11
163HL_25197.11
164HL_58786.11
165HL_59604.11
166HL_97499.11
167HL_35004.11
168HL_03431.11
169HL_00238.11
170HL_26579.11
171HL_57843.11
172HL_91613.11
173HL_62970.11
174HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
175HL_33277.11
176HL_10116.11Kink-turn-like Hairpin Loop
177HL_33524.11tRNA T-loop distorted by RS binding
178HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
179HL_27831.11
180HL_37962.11
181HL_93206.11
182HL_44522.11
183HL_84289.11
184HL_88960.11
185HL_85753.11
186HL_62880.11
187HL_66467.11
188HL_56775.11
189HL_33640.11
190HL_79390.11
191HL_10842.11
192HL_57217.11cHS platform Intercalation Site
193HL_81780.11
194HL_90365.115S rRNA Loop C from D.radiodurans
195HL_39422.11
196HL_66877.11cSH GU/cWS double platform, intercalation site
197HL_67000.11
198HL_96192.11
199HL_47337.11
200HL_68733.11LSU Yeast Hairpin Loop
201HL_69403.11GNRA-like
202HL_55202.11U2B"-U2A" binding hairpin loop
203HL_60420.11
204HL_59610.11
205HL_23522.11
206HL_30128.11
207HL_48480.11
208HL_20806.11
209HL_20914.11
210HL_05113.11
211HL_77981.11
212HL_66880.11
213HL_44390.11
214HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
215HL_78420.11
216HL_90102.11Kink-turn-like Hairpin Loop
217HL_82288.11
218HL_55543.11
219HL_81661.11tRNA D-loop
220HL_93567.11
221HL_99779.11
222HL_15771.11
223HL_42969.11
224HL_76027.11
225HL_27397.11
226HL_56809.11
227HL_63304.11
228HL_25175.11
229HL_95716.11
230HL_36842.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.2222
2HL_72498.362
3HL_39895.234
4HL_91226.217Kissing Hairpin motif
5HL_68081.210LSU Helix 20 Hairpin loop
6HL_28436.29LSU Helix 96 (H96) Hairpin Loop
7HL_82294.28SSU Helix 37 (h37) Hairpin loop.

Removed motif groups

#Motif idInstancesDescription
1HL_76014.12
2HL_81241.12
3HL_85369.12
4HL_08091.12
5HL_16860.11
6HL_58149.11
7HL_66090.11
8HL_03805.11

Added motif groups