Changes in PDB files used for clustering

Release 0.8 has 203 PDB files, release 1.0 has 206 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.0: 3W3S, 4B5R, 4HXH.

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 0.8 has 246 motif groups, release 1.0 has 252 motif groups, 227 of them are identical.

9 motif groups were updated, 10 groups are present only in release 0.8, 16 groups are only in release 1.0.

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_39895.334UNCG Hairpin motifs
2HL_18781.121Double sheared (tSH) with U-turn
3HL_91226.217Kissing Hairpin motif
4HL_97270.115T-loops with 1 bulged base
5HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_48039.111MS2 virus RNA Hairpin
7HL_80459.111
8HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
9HL_49036.110GNRA with one bulged base
10HL_56824.110LSU Helix 60A. LSU Helix 63A.
11HL_46175.11016S helix 23 and 24 hairpin loops
12HL_68081.210LSU Helix 20 Hairpin loop
13HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
14HL_28436.29LSU Helix 96 (H96) Hairpin Loop
15HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
18HL_82294.28SSU Helix 37 (h37) Hairpin loop.
19HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
20HL_34027.175S Loop C - Upper part of Hairpin Loop.
21HL_46489.16LSU H89 Hairpin Loop
22HL_42677.16
23HL_39942.16LSU Helix 91 (H91) Hairpin Loop
24HL_70420.16LSU Helix 97 Hairpin loop
25HL_18156.16LSU Helix 72 (H72) Hairpin Loop
26HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
28HL_75579.16
29HL_87136.16LSU Helix 39A Hairpin loop
30HL_41833.16LSU Helix 81 (H81) Hairpin Loop
31HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
32HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
33HL_45018.35Hairpin-Hairpin Interacting HL
34HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
35HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
36HL_72273.15tRNA D-loop
37HL_88311.15LSU Helix 35 (H35) Hairpin Loop
38HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_98523.14GNRA-like. Closed by tSH UC.
41HL_29831.14GNRA-like with bulged base.
42HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
43HL_64543.14SSU Helix 31 (h31) Hairpin Loop
44HL_62881.14RNase P Structured Hairpin Loop
45HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
46HL_41827.13
47HL_61547.23
48HL_23182.13
49HL_46794.23
50HL_73023.13Two base, cross-stacked hairpin loop
51HL_90579.13
52HL_78361.13
53HL_08382.23
54HL_42077.23LSU Helix 28 (H28) Hairpin Loop
55HL_27429.23
56HL_19221.23
57HL_82253.13
58HL_13707.23cSH AA Platform containing Hairpin Loop
59HL_58083.23
60HL_80492.23tRNA D-loop
61HL_32644.13LSU Helix 69 (H69) Hairpin Loop
62HL_54751.13
63HL_42687.23
64HL_25124.13tSW GA closed tetraloops
65HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
66HL_98833.13
67HL_53753.12
68HL_94578.12
69HL_68697.12
70HL_81752.12
71HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
72HL_49210.12
73HL_05510.12
74HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
75HL_65924.12
76HL_23290.12
77HL_05361.12
78HL_57014.12
79HL_03791.12
80HL_06122.12
81HL_24711.12
82HL_24473.32tRNA D-loop
83HL_06312.12
84HL_05797.12
85HL_76105.12
86HL_76766.12
87HL_63823.12
88HL_84353.12
89HL_12595.12
90HL_22614.12
91HL_26057.12
92HL_98577.12
93HL_16770.12
94HL_57904.12
95HL_38130.22
96HL_42553.12
97HL_19399.12
98HL_67692.12
99HL_75575.12
100HL_19905.12
101HL_77555.12
102HL_81555.12
103HL_49267.12
104HL_33451.12
105HL_87554.12
106HL_99633.12
107HL_96915.12
108HL_38138.11
109HL_33640.11
110HL_93567.11
111HL_03431.11
112HL_00238.11
113HL_44522.11
114HL_68579.11
115HL_85753.11
116HL_96192.11
117HL_47337.11
118HL_68733.11LSU Yeast Hairpin Loop
119HL_97784.11
120HL_23522.11
121HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
122HL_45411.11
123HL_59604.11
124HL_97499.11
125HL_35004.11
126HL_93206.11
127HL_39422.11
128HL_79902.11
129HL_67000.11
130HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
131HL_78420.11
132HL_90102.11Kink-turn-like Hairpin Loop
133HL_18011.11
134HL_66900.11
135HL_33524.11tRNA T-loop distorted by RS binding
136HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
137HL_56775.11
138HL_07315.11
139HL_37962.11
140HL_81780.11
141HL_90365.115S rRNA Loop C from D.radiodurans
142HL_42969.11
143HL_57843.11
144HL_44390.11
145HL_63304.11
146HL_25175.11
147HL_95716.11
148HL_71607.11
149HL_10116.11Kink-turn-like Hairpin Loop
150HL_81661.11tRNA D-loop
151HL_17468.11
152HL_53789.11
153HL_25195.11
154HL_57217.11cHS platform Intercalation Site
155HL_84888.11T-loop like but without tWH UA
156HL_19132.11
157HL_56809.11
158HL_00090.11
159HL_55272.11
160HL_97971.11
161HL_82243.11
162HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
163HL_59610.11
164HL_55543.11
165HL_24707.11
166HL_58786.11
167HL_20806.11
168HL_20914.11
169HL_15771.11
170HL_88960.11
171HL_27819.11
172HL_67761.11
173HL_53015.11
174HL_78228.11
175HL_35200.11
176HL_69403.11GNRA-like
177HL_17537.11
178HL_25197.11
179HL_63411.11
180HL_68435.11
181HL_58601.11
182HL_66877.11cSH GU/cWS double platform, intercalation site
183HL_12706.11
184HL_13786.11
185HL_04194.11
186HL_75850.11
187HL_39486.11
188HL_82288.11
189HL_85018.11
190HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
191HL_78507.11
192HL_87223.11
193HL_65071.11
194HL_58223.11
195HL_27397.11
196HL_70912.11
197HL_62970.11
198HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
199HL_33277.11
200HL_36842.11
201HL_19452.11tRNA D-loop
202HL_55202.11U2B"-U2A" binding hairpin loop
203HL_65802.11
204HL_35865.11
205HL_30128.11
206HL_48480.11
207HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
208HL_63690.11
209HL_02479.11
210HL_61061.11
211HL_26579.11
212HL_84289.11
213HL_34440.11
214HL_62880.11
215HL_66467.11
216HL_99207.11Tetrahymena LSU hairpin poorly modeled

Updated motif groups

#Motif idInstancesDescription
1HL_67042.4225GNRA Hairpin motifs
2HL_72498.563T-loops with two bulged bases
3HL_74465.212tRNA Anti-Codon loop
4HL_17723.210LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
5HL_01926.26LSU Helix 71 (H71) Hairpin Loop.
6HL_06643.25tRNA D-loop. Sec tRNA
7HL_95423.25UNCG-like. cWW Closing pair.
8HL_76036.23LSU Helix 8 (H8) Hairpin Loop
9HL_64371.22

Removed motif groups

#Motif idInstancesDescription
1HL_19261.15SSU Central Pseudoknot (forms helix 2)
2HL_20739.13
3HL_53664.13Double tSH (double sheared) with bulged base
4HL_14013.12
5HL_93015.12
6HL_46981.12
7HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
8HL_70459.12
9HL_27831.11
10HL_01987.11

Added motif groups

#Motif idInstancesDescription
1HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
2HL_47784.14SSU Central Pseudoknot (forms helix 2)
3HL_74686.13SSU Central Pseudoknot (forms helix 2)
4HL_67367.12
5HL_62967.12
6HL_13105.11
7HL_19226.11
8HL_29084.11
9HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
10HL_80746.11
11HL_85138.11LSU Helix 8 (H8) Hairpin Loop
12HL_52393.11Double tSH (double sheared) with bulged base
13HL_60203.11
14HL_12984.11