Changes in PDB files used for clustering

Release 1.9 has 221 PDB files, release 1.10 has 225 PDB files, 221 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.10: 3WFS, 4M30, 4M4O, 4M6D.

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 1.9 has 253 motif groups, release 1.10 has 253 motif groups, 248 of them are identical.

4 motif groups were updated, 1 groups are present only in release 1.9, 1 groups are only in release 1.10.

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_67042.10229GNRA Hairpin motifs
2HL_39895.635UNCG Hairpin motifs
3HL_18781.420Double sheared (tSH) with U-turn
4HL_91226.317Kissing Hairpin motif
5HL_97270.315T-loops with 1 bulged base
6HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_49036.312GNRA with one bulged base
8HL_48039.211MS2 virus RNA Hairpin
9HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
10HL_68081.310LSU Helix 20 Hairpin loop
11HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_46175.21016S helix 23 and 24 hairpin loops
13HL_56824.210LSU Helix 60A. LSU Helix 63A.
14HL_80459.39
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_34027.285S Loop C - Upper part of Hairpin Loop.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_42677.27
23HL_70420.26LSU Helix 97 Hairpin loop
24HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
25HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
26HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
27HL_18156.26LSU Helix 72 (H72) Hairpin Loop
28HL_75579.26
29HL_87136.26LSU Helix 39A Hairpin loop
30HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
31HL_41833.26LSU Helix 81 (H81) Hairpin Loop
32HL_46489.26LSU H89 Hairpin Loop
33HL_39942.26LSU Helix 91 (H91) Hairpin Loop
34HL_57514.26Two base, cross-stacked hairpin loop
35HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
36HL_88311.25LSU Helix 35 (H35) Hairpin Loop
37HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
38HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
39HL_06643.25tRNA D-loop. Sec tRNA
40HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42HL_45018.35Hairpin-Hairpin Interacting HL
43HL_72273.15tRNA D-loop
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_47784.24SSU Central Pseudoknot (forms helix 2)
47HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
48HL_25124.24tSW GA closed tetraloops
49HL_64543.24SSU Helix 31 (h31) Hairpin Loop
50HL_62881.14RNase P Structured Hairpin Loop
51HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
52HL_98523.24GNRA-like. Closed by tSH UC.
53HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
54HL_29831.14GNRA-like with bulged base.
55HL_11376.14LSU Helix 8 (H8) Hairpin Loop
56HL_19221.23
57HL_76036.33LSU Helix 8 (H8) Hairpin Loop
58HL_90579.33LSU Helix 69 (H69) Hairpin Loop
59HL_13707.23cSH AA Platform containing Hairpin Loop
60HL_98833.33
61HL_58083.23
62HL_74686.13SSU Central Pseudoknot (forms helix 2)
63HL_27429.33
64HL_78361.13
65HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
66HL_41827.13
67HL_80492.23tRNA D-loop
68HL_06997.23
69HL_08382.23
70HL_42077.23LSU Helix 28 (H28) Hairpin Loop
71HL_23182.13
72HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
73HL_35619.23
74HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
75HL_68697.23
76HL_91693.12
77HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
78HL_24473.32tRNA D-loop
79HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
80HL_18587.12
81HL_62967.12
82HL_42094.12
83HL_05361.12
84HL_64371.22
85HL_63941.12
86HL_54751.22
87HL_17790.12UNCG-like. cWW Closing pair.
88HL_99633.12
89HL_93771.12tRNA T-loop distorted by RS binding
90HL_74505.12
91HL_38130.22
92HL_26495.12
93HL_06122.12
94HL_65249.12
95HL_42553.12
96HL_21545.12LSU Helix 96 (H96) Hairpin Loop
97HL_86398.12
98HL_96915.12
99HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
100HL_84353.12
101HL_65924.12
102HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
103HL_33451.12
104HL_50312.12
105HL_19528.12
106HL_87554.12
107HL_91872.12
108HL_16770.12
109HL_49210.12
110HL_32644.22LSU Helix 69 (H69) Hairpin Loop
111HL_98577.12
112HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
113HL_23129.12
114HL_60200.12
115HL_24711.12
116HL_23290.12
117HL_94578.12
118HL_19399.12
119HL_74559.12Two base, cross-stacked hairpin loop
120HL_90542.12
121HL_55202.11U2B"-U2A" binding hairpin loop
122HL_59610.11
123HL_45411.11
124HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
125HL_60203.11
126HL_44522.11
127HL_66877.11cSH GU/cWS double platform, intercalation site
128HL_56809.11
129HL_93263.11
130HL_95716.11
131HL_82243.11
132HL_10116.11Kink-turn-like Hairpin Loop
133HL_73465.11
134HL_42345.11
135HL_52116.11
136HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
137HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
138HL_76585.11
139HL_87223.11
140HL_39422.11
141HL_27397.11
142HL_07915.11
143HL_00090.11
144HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
145HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
146HL_78228.11
147HL_97971.11
148HL_69403.11GNRA-like
149HL_46570.11
150HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
151HL_96994.11
152HL_73972.11
153HL_53789.11
154HL_25195.11
155HL_59604.11
156HL_97499.11
157HL_65071.11
158HL_84289.11
159HL_34440.11
160HL_27819.11
161HL_67761.11
162HL_63304.11
163HL_75850.11
164HL_35200.11
165HL_82288.11
166HL_83865.11
167HL_01418.11
168HL_24108.11
169HL_84768.11
170HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
171HL_24707.11
172HL_37962.11
173HL_52540.11
174HL_05113.11
175HL_68579.11
176HL_12706.11
177HL_13786.11
178HL_55272.11
179HL_47337.11
180HL_39486.11
181HL_36842.11
182HL_23195.11
183HL_20028.11
184HL_59182.11
185HL_38138.11
186HL_35865.11
187HL_25197.11
188HL_28676.11
189HL_57217.11cHS platform Intercalation Site
190HL_95049.11Two base, cross-stacked hairpin loop
191HL_42969.11
192HL_79902.11
193HL_70912.11
194HL_53015.11
195HL_78420.11
196HL_33277.11
197HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
198HL_59225.11
199HL_33640.11
200HL_65802.11
201HL_20806.11
202HL_68435.11
203HL_84888.11T-loop like but without tWH UA
204HL_57843.11
205HL_03785.11LSU Helix 8 (H8) Hairpin Loop
206HL_25175.11
207HL_68733.11LSU Yeast Hairpin Loop
208HL_66467.11
209HL_99207.11Tetrahymena LSU hairpin poorly modeled
210HL_17537.11
211HL_99584.11
212HL_29196.11
213HL_56775.11
214HL_30128.11
215HL_48480.11
216HL_99779.11
217HL_19226.11
218HL_58223.11
219HL_19132.11
220HL_62970.11
221HL_76679.11
222HL_90102.11Kink-turn-like Hairpin Loop
223HL_97784.11
224HL_85018.11
225HL_08203.11
226HL_77692.11tRNA D-loop
227HL_93567.11
228HL_78507.11
229HL_26579.11
230HL_58601.11
231HL_88960.11
232HL_44390.11
233HL_67000.11
234HL_62880.11
235HL_04194.11
236HL_93530.11
237HL_19452.11tRNA D-loop
238HL_30008.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.1266T-loops with two bulged bases
2HL_74465.513tRNA Anti-Codon loop
3HL_27271.212LSU Helix 96 (H96) Hairpin Loop
4HL_76766.43

Removed motif groups

#Motif idInstancesDescription
1HL_42687.43

Added motif groups

#Motif idInstancesDescription
1HL_86115.14