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_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_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_46489.16LSU H89 Hairpin Loop
27HL_39942.16LSU Helix 91 (H91) Hairpin Loop
28HL_70420.16LSU Helix 97 Hairpin loop
29HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
30HL_18156.16LSU Helix 72 (H72) Hairpin Loop
31HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
32HL_42677.16
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_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_19261.15SSU Central Pseudoknot (forms helix 2)
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_98523.14GNRA-like. Closed by tSH UC.
47HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
48HL_95423.14UNCG-like. cWW Closing pair.
49HL_64543.14SSU Helix 31 (h31) Hairpin Loop
50HL_45018.24
51HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
52HL_62881.14RNase P Structured Hairpin Loop
53HL_29831.14GNRA-like with bulged base.
54HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
55HL_76036.13LSU Helix 8 (H8) Hairpin Loop
56HL_90579.13
57HL_46794.23
58HL_80492.23tRNA D-loop
59HL_53664.13Double tSH (double sheared) with bulged base
60HL_27429.23
61HL_25124.13tSW GA closed tetraloops
62HL_54751.13
63HL_13707.23cSH AA Platform containing Hairpin Loop
64HL_42687.23
65HL_19221.23
66HL_78361.13
67HL_41827.13
68HL_98833.13
69HL_61547.23
70HL_58083.23
71HL_82253.13
72HL_32644.13LSU Helix 69 (H69) Hairpin Loop
73HL_42077.23LSU Helix 28 (H28) Hairpin Loop
74HL_64371.13
75HL_73023.13Two base, cross-stacked hairpin loop
76HL_20739.13
77HL_23182.13
78HL_24711.12
79HL_49267.12
80HL_98577.12
81HL_70459.12
82HL_96915.12
83HL_49210.12
84HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
85HL_99633.12
86HL_68697.12
87HL_81752.12
88HL_23290.12
89HL_19905.12
90HL_77555.12
91HL_42553.12
92HL_03791.12
93HL_12595.12
94HL_24473.32tRNA D-loop
95HL_81555.12
96HL_06312.12
97HL_57014.12
98HL_05510.12
99HL_44467.12
100HL_53753.12
101HL_57904.12
102HL_94578.12
103HL_33451.12
104HL_14013.12
105HL_05797.12
106HL_06122.12
107HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
108HL_46981.12
109HL_19399.12
110HL_76105.12
111HL_76766.12
112HL_63823.12
113HL_84353.12
114HL_65924.12
115HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
116HL_38130.22
117HL_93015.12
118HL_67692.12
119HL_26057.12
120HL_16770.12
121HL_75575.12
122HL_05361.12
123HL_87554.12
124HL_33277.11
125HL_99207.11Tetrahymena LSU hairpin poorly modeled
126HL_98233.11
127HL_38898.11
128HL_23522.11
129HL_25197.11
130HL_58786.11
131HL_25195.11
132HL_63690.11
133HL_65071.11
134HL_68435.11
135HL_88960.11
136HL_85753.11
137HL_62880.11
138HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
139HL_66467.11
140HL_97784.11
141HL_17008.11Nova-2 KH3 domain binding hairpin
142HL_59610.11
143HL_55543.11
144HL_81661.11tRNA D-loop
145HL_27831.11
146HL_59604.11
147HL_97499.11
148HL_02479.11
149HL_61061.11
150HL_58223.11
151HL_58601.11
152HL_66877.11cSH GU/cWS double platform, intercalation site
153HL_67000.11
154HL_96192.11
155HL_68733.11LSU Yeast Hairpin Loop
156HL_66900.11
157HL_17468.11
158HL_37962.11
159HL_35004.11
160HL_03431.11
161HL_00238.11
162HL_26579.11
163HL_66880.11
164HL_44390.11
165HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
166HL_47337.11
167HL_90102.11Kink-turn-like Hairpin Loop
168HL_71607.11
169HL_10116.11Kink-turn-like Hairpin Loop
170HL_30128.11
171HL_48480.11
172HL_57217.11cHS platform Intercalation Site
173HL_93206.11
174HL_44522.11
175HL_84289.11
176HL_27397.11
177HL_56809.11
178HL_63304.11
179HL_78420.11
180HL_95716.11
181HL_82243.11
182HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
183HL_33524.11tRNA T-loop distorted by RS binding
184HL_93567.11
185HL_20806.11
186HL_81780.11
187HL_90365.115S rRNA Loop C from D.radiodurans
188HL_39422.11
189HL_34440.11
190HL_27819.11
191HL_00090.11
192HL_55272.11
193HL_25175.11
194HL_97971.11
195HL_69403.11GNRA-like
196HL_17537.11
197HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
198HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
199HL_99779.11
200HL_20914.11
201HL_05113.11
202HL_79902.11
203HL_30731.11
204HL_12706.11
205HL_67761.11
206HL_53015.11
207HL_35200.11
208HL_82288.11
209HL_85018.11
210HL_55202.11U2B"-U2A" binding hairpin loop
211HL_38138.11
212HL_07315.11
213HL_45411.11
214HL_78507.11
215HL_15771.11
216HL_42969.11
217HL_57843.11
218HL_68579.11
219HL_70912.11
220HL_13786.11
221HL_04194.11
222HL_78228.11
223HL_39486.11
224HL_36842.11
225HL_19452.11tRNA D-loop
226HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
227HL_56775.11
228HL_33640.11
229HL_65802.11
230HL_35865.11
231HL_24707.11
232HL_53789.11
233HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
234HL_87223.11
235HL_00721.11
236HL_63411.11
237HL_45358.11Double hairpin loop based on GGA triple
238HL_84888.11T-loop like but without tWH UA
239HL_19132.11
240HL_91613.11
241HL_62970.11
242HL_01987.11
243HL_75850.11

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