Changes in PDB files used for clustering

Release 1.9 has 220 PDB files, release 1.10 has 224 PDB files, 220 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_46175.21016S helix 23 and 24 hairpin loops
10HL_56824.210LSU Helix 60A. LSU Helix 63A.
11HL_68081.310LSU Helix 20 Hairpin loop
12HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
13HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_80459.39
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop 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_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22HL_42677.27
23HL_18156.26LSU Helix 72 (H72) Hairpin Loop
24HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25HL_46489.26LSU H89 Hairpin Loop
26HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
27HL_39942.26LSU Helix 91 (H91) Hairpin Loop
28HL_70420.26LSU Helix 97 Hairpin loop
29HL_57514.26Two base, cross-stacked hairpin loop
30HL_75579.26
31HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
32HL_41833.26LSU Helix 81 (H81) Hairpin Loop
33HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
34HL_87136.26LSU Helix 39A Hairpin loop
35HL_88311.25LSU Helix 35 (H35) Hairpin Loop
36HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
37HL_72273.15tRNA D-loop
38HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
41HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
42HL_45018.35Hairpin-Hairpin Interacting HL
43HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44HL_06643.25tRNA D-loop. Sec tRNA
45HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
46HL_29831.14GNRA-like with bulged base.
47HL_62881.14RNase P Structured Hairpin Loop
48HL_98523.24GNRA-like. Closed by tSH UC.
49HL_47784.24SSU Central Pseudoknot (forms helix 2)
50HL_11376.14LSU Helix 8 (H8) Hairpin Loop
51HL_25124.24tSW GA closed tetraloops
52HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
53HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
54HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
55HL_64543.24SSU Helix 31 (h31) Hairpin Loop
56HL_06997.23
57HL_13707.23cSH AA Platform containing Hairpin Loop
58HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
59HL_80492.23tRNA D-loop
60HL_08382.23
61HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
62HL_74686.13SSU Central Pseudoknot (forms helix 2)
63HL_41827.13
64HL_78361.13
65HL_19221.23
66HL_98833.33
67HL_27429.33
68HL_42077.23LSU Helix 28 (H28) Hairpin Loop
69HL_58083.23
70HL_23182.13
71HL_76036.33LSU Helix 8 (H8) Hairpin Loop
72HL_35619.23
73HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
74HL_68697.23
75HL_90579.33LSU Helix 69 (H69) Hairpin Loop
76HL_19528.12
77HL_23290.12
78HL_33451.12
79HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
80HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
81HL_74505.12
82HL_84353.12
83HL_18587.12
84HL_42553.12
85HL_65249.12
86HL_74559.12Two base, cross-stacked hairpin loop
87HL_87554.12
88HL_91693.12
89HL_24473.32tRNA D-loop
90HL_26495.12
91HL_49210.12
92HL_62967.12
93HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
94HL_91872.12
95HL_21545.12LSU Helix 96 (H96) Hairpin Loop
96HL_38130.22
97HL_54751.22
98HL_98577.12
99HL_16770.12
100HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
101HL_60200.12
102HL_65924.12
103HL_96915.12
104HL_05361.12
105HL_23129.12
106HL_24711.12
107HL_32644.22LSU Helix 69 (H69) Hairpin Loop
108HL_50312.12
109HL_63941.12
110HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
111HL_06122.12
112HL_19399.12
113HL_42094.12
114HL_64371.22
115HL_86398.12
116HL_90542.12
117HL_93771.12tRNA T-loop distorted by RS binding
118HL_99633.12
119HL_17790.12UNCG-like. cWW Closing pair.
120HL_94578.12
121HL_00090.11
122HL_12706.11
123HL_25195.11
124HL_29196.11
125HL_35865.11
126HL_48480.11
127HL_56809.11
128HL_59182.11
129HL_62880.11
130HL_65071.11
131HL_68733.11LSU Yeast Hairpin Loop
132HL_76679.11
133HL_87223.11
134HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
135HL_97784.11
136HL_01418.11
137HL_07915.11
138HL_24108.11
139HL_25197.11
140HL_33640.11
141HL_36842.11
142HL_53015.11
143HL_59225.11
144HL_67000.11
145HL_69403.11GNRA-like
146HL_77692.11tRNA D-loop
147HL_84768.11
148HL_95049.11Two base, cross-stacked hairpin loop
149HL_97971.11
150HL_13786.11
151HL_20806.11
152HL_30008.11
153HL_37962.11
154HL_46570.11
155HL_53789.11
156HL_57217.11cHS platform Intercalation Site
157HL_59604.11
158HL_78228.11
159HL_82243.11
160HL_84888.11T-loop like but without tWH UA
161HL_95716.11
162HL_03785.11LSU Helix 8 (H8) Hairpin Loop
163HL_10116.11Kink-turn-like Hairpin Loop
164HL_19132.11
165HL_26579.11
166HL_30128.11
167HL_42969.11
168HL_47337.11
169HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
170HL_59610.11
171HL_62970.11
172HL_65802.11
173HL_67761.11
174HL_70912.11
175HL_82288.11
176HL_85018.11
177HL_93263.11
178HL_04194.11
179HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
180HL_24707.11
181HL_27397.11
182HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
183HL_38138.11
184HL_44390.11
185HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
186HL_55202.11U2B"-U2A" binding hairpin loop
187HL_57843.11
188HL_63304.11
189HL_78420.11
190HL_88960.11
191HL_93530.11
192HL_17537.11
193HL_19226.11
194HL_34440.11
195HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
196HL_44522.11
197HL_55272.11
198HL_60203.11
199HL_68435.11
200HL_75850.11
201HL_78507.11
202HL_90102.11Kink-turn-like Hairpin Loop
203HL_93567.11
204HL_96994.11
205HL_99207.11Tetrahymena LSU hairpin poorly modeled
206HL_27819.11
207HL_33277.11
208HL_35200.11
209HL_39422.11
210HL_52116.11
211HL_58223.11
212HL_66467.11
213HL_68579.11
214HL_73465.11
215HL_83865.11
216HL_19452.11tRNA D-loop
217HL_23195.11
218HL_25175.11
219HL_28676.11
220HL_39486.11
221HL_42345.11
222HL_45411.11
223HL_52540.11
224HL_56775.11
225HL_58601.11
226HL_66877.11cSH GU/cWS double platform, intercalation site
227HL_73972.11
228HL_76585.11
229HL_79902.11
230HL_84289.11
231HL_97499.11

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