Changes in PDB files used for clustering

Release 0.6 has 207 PDB files, release 0.7 has 207 PDB files, 206 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 0.7: 3ZD3.

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 0.6 has 245 motif groups, release 0.7 has 246 motif groups, 243 of them are identical.

1 motif groups were updated, 1 groups are present only in release 0.6, 2 groups are only in release 0.7.

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_68081.210LSU Helix 20 Hairpin loop
12HL_46175.11016S helix 23 and 24 hairpin loops
13HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
14HL_49036.110GNRA with one bulged base
15HL_56824.110LSU Helix 60A. LSU Helix 63A.
16HL_28436.29LSU Helix 96 (H96) Hairpin Loop
17HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
18HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_82294.28SSU Helix 37 (h37) Hairpin loop.
21HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
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_70420.16LSU Helix 97 Hairpin loop
27HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
28HL_18156.16LSU Helix 72 (H72) Hairpin Loop
29HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_42677.16
31HL_75579.16
32HL_87136.16LSU Helix 39A Hairpin loop
33HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
34HL_41833.16LSU Helix 81 (H81) Hairpin Loop
35HL_46489.16LSU H89 Hairpin Loop
36HL_39942.16LSU Helix 91 (H91) Hairpin Loop
37HL_88311.15LSU Helix 35 (H35) Hairpin Loop
38HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_06643.15tRNA D-loop. Sec tRNA
41HL_72273.15tRNA D-loop
42HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
43HL_19261.15SSU Central Pseudoknot (forms helix 2)
44HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_64543.14SSU Helix 31 (h31) Hairpin Loop
47HL_45018.24
48HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
49HL_62881.14RNase P Structured Hairpin Loop
50HL_29831.14GNRA-like with bulged base.
51HL_98523.14GNRA-like. Closed by tSH UC.
52HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
53HL_95423.14UNCG-like. cWW Closing pair.
54HL_53664.13Double tSH (double sheared) with bulged base
55HL_27429.23
56HL_25124.13tSW GA closed tetraloops
57HL_54751.13
58HL_13707.23cSH AA Platform containing Hairpin Loop
59HL_42687.23
60HL_19221.23
61HL_78361.13
62HL_41827.13
63HL_98833.13
64HL_61547.23
65HL_58083.23
66HL_82253.13
67HL_32644.13LSU Helix 69 (H69) Hairpin Loop
68HL_42077.23LSU Helix 28 (H28) Hairpin Loop
69HL_64371.13
70HL_73023.13Two base, cross-stacked hairpin loop
71HL_20739.13
72HL_23182.13
73HL_76036.13LSU Helix 8 (H8) Hairpin Loop
74HL_90579.13
75HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
76HL_46794.23
77HL_80492.23tRNA D-loop
78HL_81752.12
79HL_23290.12
80HL_19905.12
81HL_77555.12
82HL_42553.12
83HL_03791.12
84HL_68697.12
85HL_12595.12
86HL_24473.32tRNA D-loop
87HL_81555.12
88HL_06312.12
89HL_57014.12
90HL_05510.12
91HL_44467.12
92HL_53753.12
93HL_57904.12
94HL_94578.12
95HL_33451.12
96HL_14013.12
97HL_05797.12
98HL_06122.12
99HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
100HL_46981.12
101HL_19399.12
102HL_76105.12
103HL_76766.12
104HL_63823.12
105HL_84353.12
106HL_65924.12
107HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
108HL_38130.22
109HL_93015.12
110HL_67692.12
111HL_26057.12
112HL_16770.12
113HL_75575.12
114HL_05361.12
115HL_87554.12
116HL_24711.12
117HL_49267.12
118HL_98577.12
119HL_70459.12
120HL_49210.12
121HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
122HL_99633.12
123HL_96915.12
124HL_17468.11
125HL_37962.11
126HL_35004.11
127HL_03431.11
128HL_00238.11
129HL_26579.11
130HL_66880.11
131HL_44390.11
132HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
133HL_47337.11
134HL_68733.11LSU Yeast Hairpin Loop
135HL_66900.11
136HL_30128.11
137HL_48480.11
138HL_57217.11cHS platform Intercalation Site
139HL_93206.11
140HL_44522.11
141HL_84289.11
142HL_27397.11
143HL_56809.11
144HL_63304.11
145HL_78420.11
146HL_90102.11Kink-turn-like Hairpin Loop
147HL_71607.11
148HL_10116.11Kink-turn-like Hairpin Loop
149HL_33524.11tRNA T-loop distorted by RS binding
150HL_93567.11
151HL_20806.11
152HL_81780.11
153HL_90365.115S rRNA Loop C from D.radiodurans
154HL_39422.11
155HL_34440.11
156HL_27819.11
157HL_00090.11
158HL_55272.11
159HL_25175.11
160HL_95716.11
161HL_82243.11
162HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
163HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
164HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
165HL_99779.11
166HL_20914.11
167HL_05113.11
168HL_79902.11
169HL_30731.11
170HL_12706.11
171HL_67761.11
172HL_53015.11
173HL_97971.11
174HL_69403.11GNRA-like
175HL_17537.11
176HL_55202.11U2B"-U2A" binding hairpin loop
177HL_38138.11
178HL_07315.11
179HL_45411.11
180HL_78507.11
181HL_15771.11
182HL_42969.11
183HL_57843.11
184HL_68579.11
185HL_70912.11
186HL_13786.11
187HL_04194.11
188HL_78228.11
189HL_35200.11
190HL_82288.11
191HL_85018.11
192HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
193HL_56775.11
194HL_33640.11
195HL_65802.11
196HL_35865.11
197HL_24707.11
198HL_53789.11
199HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
200HL_87223.11
201HL_00721.11
202HL_63411.11
203HL_45358.11Double hairpin loop based on GGA triple
204HL_84888.11T-loop like but without tWH UA
205HL_19132.11
206HL_91613.11
207HL_62970.11
208HL_01987.11
209HL_75850.11
210HL_39486.11
211HL_36842.11
212HL_19452.11tRNA D-loop
213HL_38898.11
214HL_23522.11
215HL_25197.11
216HL_58786.11
217HL_25195.11
218HL_63690.11
219HL_65071.11
220HL_68435.11
221HL_88960.11
222HL_85753.11
223HL_62880.11
224HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
225HL_33277.11
226HL_99207.11Tetrahymena LSU hairpin poorly modeled
227HL_98233.11
228HL_17008.11Nova-2 KH3 domain binding hairpin
229HL_59610.11
230HL_55543.11
231HL_81661.11tRNA D-loop
232HL_27831.11
233HL_59604.11
234HL_97499.11
235HL_02479.11
236HL_61061.11
237HL_58223.11
238HL_58601.11
239HL_66877.11cSH GU/cWS double platform, intercalation site
240HL_67000.11
241HL_96192.11
242HL_66467.11
243HL_97784.11

Updated motif groups

#Motif idInstancesDescription
1HL_08382.23

Removed motif groups

#Motif idInstancesDescription
1HL_88640.12

Added motif groups

#Motif idInstancesDescription
1HL_22614.12
2HL_18011.11