Changes in PDB files used for clustering

Release 0.5 has 201 PDB files, release 0.6 has 202 PDB files, 198 of them are identical.

3 equivalence classes changed representatives: 3U4M3UMY, 3G784FAW, 2FK64GCW.

1 new structures in release 0.6: 4FY3.

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 0.5 has 247 motif groups, release 0.6 has 245 motif groups, 227 of them are identical.

4 motif groups were updated, 16 groups are present only in release 0.5, 14 groups are only in release 0.6.

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_91226.217Kissing Hairpin motif
3HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
4HL_97270.115T-loops with 1 bulged base
5HL_48039.111MS2 virus RNA Hairpin
6HL_80459.111
7HL_74465.111tRNA Anti-Codon loop
8HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
9HL_56824.110LSU Helix 60A. LSU Helix 63A.
10HL_68081.210LSU Helix 20 Hairpin loop
11HL_46175.11016S helix 23 and 24 hairpin loops
12HL_49036.110GNRA with one bulged base
13HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_28436.29LSU Helix 96 (H96) Hairpin Loop
16HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
17HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_82294.28SSU Helix 37 (h37) Hairpin loop.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_34027.175S Loop C - Upper part of Hairpin Loop.
21HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
22HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
23HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
24HL_41833.16LSU Helix 81 (H81) Hairpin Loop
25HL_70420.16LSU Helix 97 Hairpin loop
26HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
27HL_87136.16LSU Helix 39A Hairpin loop
28HL_18156.16LSU Helix 72 (H72) Hairpin Loop
29HL_42677.16
30HL_46489.16LSU H89 Hairpin Loop
31HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
32HL_39942.16LSU Helix 91 (H91) Hairpin Loop
33HL_75579.16
34HL_19261.15SSU Central Pseudoknot (forms helix 2)
35HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
36HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
37HL_06643.15tRNA D-loop. Sec tRNA
38HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_72273.15tRNA D-loop
41HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42HL_88311.15LSU Helix 35 (H35) Hairpin Loop
43HL_29831.14GNRA-like with bulged base.
44HL_62881.14RNase P Structured Hairpin Loop
45HL_45018.24
46HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
47HL_95423.14UNCG-like. cWW Closing pair.
48HL_98523.14GNRA-like. Closed by tSH UC.
49HL_08382.14
50HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
51HL_64543.14SSU Helix 31 (h31) Hairpin Loop
52HL_42077.23LSU Helix 28 (H28) Hairpin Loop
53HL_82253.13
54HL_32644.13LSU Helix 69 (H69) Hairpin Loop
55HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
56HL_53664.13Double tSH (double sheared) with bulged base
57HL_76036.13LSU Helix 8 (H8) Hairpin Loop
58HL_20739.13
59HL_13707.23cSH AA Platform containing Hairpin Loop
60HL_27429.23
61HL_54751.13
62HL_80492.23tRNA D-loop
63HL_90579.13
64HL_25124.13tSW GA closed tetraloops
65HL_42687.23
66HL_46794.23
67HL_73023.13Two base, cross-stacked hairpin loop
68HL_98833.13
69HL_23182.13
70HL_64371.13
71HL_78361.13
72HL_19221.23
73HL_41827.13
74HL_58083.23
75HL_05510.12
76HL_38130.22
77HL_67692.12
78HL_88640.12
79HL_05797.12
80HL_16770.12
81HL_19399.12
82HL_24473.32tRNA D-loop
83HL_26057.12
84HL_70459.12
85HL_94578.12
86HL_06122.12
87HL_19905.12
88HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
89HL_65924.12
90HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
91HL_42553.12
92HL_57014.12
93HL_76105.12
94HL_24711.12
95HL_76766.12
96HL_98577.12
97HL_03791.12
98HL_33451.12
99HL_49210.12
100HL_63823.12
101HL_81555.12
102HL_87554.12
103HL_14013.12
104HL_46981.12
105HL_49267.12
106HL_57904.12
107HL_96915.12
108HL_05361.12
109HL_23290.12
110HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
111HL_99633.12
112HL_00090.11
113HL_15771.11
114HL_23522.11
115HL_25197.11
116HL_44522.11
117HL_56775.11
118HL_58223.11
119HL_65071.11
120HL_78507.11
121HL_82243.11
122HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
123HL_97499.11
124HL_00238.11
125HL_30128.11
126HL_38138.11
127HL_53015.11
128HL_56809.11
129HL_58601.11
130HL_62970.11
131HL_65802.11
132HL_67761.11
133HL_75850.11
134HL_85753.11
135HL_88960.11
136HL_97784.11
137HL_12706.11
138HL_17468.11
139HL_26579.11
140HL_34440.11
141HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
142HL_45411.11
143HL_58786.11
144HL_63304.11
145HL_70912.11
146HL_79902.11
147HL_82288.11
148HL_90102.11Kink-turn-like Hairpin Loop
149HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
150HL_97971.11
151HL_02479.11
152HL_24707.11
153HL_27397.11
154HL_33277.11
155HL_35004.11
156HL_39422.11
157HL_48480.11
158HL_53789.11
159HL_59604.11
160HL_63411.11
161HL_68435.11
162HL_90365.115S rRNA Loop C from D.radiodurans
163HL_03431.11
164HL_07315.11
165HL_20806.11
166HL_35200.11
167HL_39486.11
168HL_57217.11cHS platform Intercalation Site
169HL_59610.11
170HL_63690.11
171HL_66467.11
172HL_68579.11
173HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
174HL_87223.11
175HL_95716.11
176HL_13786.11
177HL_20914.11
178HL_27819.11
179HL_35865.11
180HL_55202.11U2B"-U2A" binding hairpin loop
181HL_57843.11
182HL_61061.11
183HL_66877.11cSH GU/cWS double platform, intercalation site
184HL_68733.11LSU Yeast Hairpin Loop
185HL_78228.11
186HL_84289.11
187HL_96192.11
188HL_04194.11
189HL_10116.11Kink-turn-like Hairpin Loop
190HL_19132.11
191HL_25175.11
192HL_27831.11
193HL_33524.11tRNA T-loop distorted by RS binding
194HL_36842.11
195HL_42969.11
196HL_55272.11
197HL_66900.11
198HL_69403.11GNRA-like
199HL_81661.11tRNA D-loop
200HL_84888.11T-loop like but without tWH UA
201HL_93206.11
202HL_99207.11Tetrahymena LSU hairpin poorly modeled
203HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
204HL_25195.11
205HL_33640.11
206HL_37962.11
207HL_44390.11
208HL_47337.11
209HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
210HL_55543.11
211HL_62880.11
212HL_67000.11
213HL_78420.11
214HL_81780.11
215HL_85018.11
216HL_93567.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.3222GNRA Hairpin motifs
2HL_72498.462T-loops with two bulged bases
3HL_39895.334UNCG Hairpin motifs
4HL_61547.23

Removed motif groups

Added motif groups

#Motif idInstancesDescription
1HL_93015.12
2HL_53753.12
3HL_68697.12
4HL_06312.12
5HL_75575.12
6HL_12595.12
7HL_77555.12
8HL_81752.12
9HL_84353.12
10HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
11HL_01987.11
12HL_71607.11
13HL_17537.11
14HL_19452.11tRNA D-loop