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_68081.310LSU Helix 20 Hairpin loop
10HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
11HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
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_82294.38SSU Helix 37 (h37) Hairpin loop.
17HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
18HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_42677.27
23HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
24HL_41833.26LSU Helix 81 (H81) Hairpin Loop
25HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
26HL_87136.26LSU Helix 39A Hairpin loop
27HL_18156.26LSU Helix 72 (H72) Hairpin Loop
28HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
29HL_46489.26LSU H89 Hairpin Loop
30HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
31HL_39942.26LSU Helix 91 (H91) Hairpin Loop
32HL_70420.26LSU Helix 97 Hairpin loop
33HL_57514.26Two base, cross-stacked hairpin loop
34HL_75579.26
35HL_72273.15tRNA D-loop
36HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
37HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
38HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
40HL_45018.35Hairpin-Hairpin Interacting HL
41HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
42HL_06643.25tRNA D-loop. Sec tRNA
43HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
44HL_88311.25LSU Helix 35 (H35) Hairpin Loop
45HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
46HL_47784.24SSU Central Pseudoknot (forms helix 2)
47HL_11376.14LSU Helix 8 (H8) Hairpin Loop
48HL_25124.24tSW GA closed tetraloops
49HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
50HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
51HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
52HL_64543.24SSU Helix 31 (h31) Hairpin Loop
53HL_29831.14GNRA-like with bulged base.
54HL_62881.14RNase P Structured Hairpin Loop
55HL_98523.24GNRA-like. Closed by tSH UC.
56HL_19221.23
57HL_98833.33
58HL_27429.33
59HL_42077.23LSU Helix 28 (H28) Hairpin Loop
60HL_58083.23
61HL_23182.13
62HL_76036.33LSU Helix 8 (H8) Hairpin Loop
63HL_35619.23
64HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
65HL_68697.23
66HL_90579.33LSU Helix 69 (H69) Hairpin Loop
67HL_06997.23
68HL_13707.23cSH AA Platform containing Hairpin Loop
69HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
70HL_80492.23tRNA D-loop
71HL_08382.23
72HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
73HL_74686.13SSU Central Pseudoknot (forms helix 2)
74HL_41827.13
75HL_78361.13
76HL_16770.12
77HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
78HL_60200.12
79HL_65924.12
80HL_96915.12
81HL_05361.12
82HL_23129.12
83HL_24711.12
84HL_32644.22LSU Helix 69 (H69) Hairpin Loop
85HL_50312.12
86HL_63941.12
87HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
88HL_06122.12
89HL_19399.12
90HL_42094.12
91HL_64371.22
92HL_86398.12
93HL_90542.12
94HL_93771.12tRNA T-loop distorted by RS binding
95HL_99633.12
96HL_17790.12UNCG-like. cWW Closing pair.
97HL_94578.12
98HL_19528.12
99HL_23290.12
100HL_33451.12
101HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
102HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
103HL_74505.12
104HL_84353.12
105HL_18587.12
106HL_42553.12
107HL_65249.12
108HL_74559.12Two base, cross-stacked hairpin loop
109HL_87554.12
110HL_91693.12
111HL_24473.32tRNA D-loop
112HL_26495.12
113HL_49210.12
114HL_62967.12
115HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
116HL_91872.12
117HL_21545.12LSU Helix 96 (H96) Hairpin Loop
118HL_38130.22
119HL_54751.22
120HL_98577.12
121HL_04194.11
122HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
123HL_24707.11
124HL_27397.11
125HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
126HL_38138.11
127HL_44390.11
128HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
129HL_55202.11U2B"-U2A" binding hairpin loop
130HL_57843.11
131HL_63304.11
132HL_78420.11
133HL_88960.11
134HL_93530.11
135HL_17537.11
136HL_19226.11
137HL_34440.11
138HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
139HL_44522.11
140HL_55272.11
141HL_60203.11
142HL_68435.11
143HL_75850.11
144HL_78507.11
145HL_90102.11Kink-turn-like Hairpin Loop
146HL_93567.11
147HL_96994.11
148HL_99207.11Tetrahymena LSU hairpin poorly modeled
149HL_27819.11
150HL_33277.11
151HL_35200.11
152HL_39422.11
153HL_52116.11
154HL_58223.11
155HL_66467.11
156HL_68579.11
157HL_73465.11
158HL_83865.11
159HL_19452.11tRNA D-loop
160HL_23195.11
161HL_25175.11
162HL_28676.11
163HL_39486.11
164HL_42345.11
165HL_45411.11
166HL_52540.11
167HL_56775.11
168HL_58601.11
169HL_66877.11cSH GU/cWS double platform, intercalation site
170HL_73972.11
171HL_76585.11
172HL_79902.11
173HL_84289.11
174HL_97499.11
175HL_00090.11
176HL_12706.11
177HL_25195.11
178HL_29196.11
179HL_35865.11
180HL_48480.11
181HL_56809.11
182HL_59182.11
183HL_62880.11
184HL_65071.11
185HL_68733.11LSU Yeast Hairpin Loop
186HL_76679.11
187HL_87223.11
188HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
189HL_97784.11
190HL_01418.11
191HL_07915.11
192HL_24108.11
193HL_25197.11
194HL_33640.11
195HL_36842.11
196HL_53015.11
197HL_59225.11
198HL_67000.11
199HL_69403.11GNRA-like
200HL_77692.11tRNA D-loop
201HL_84768.11
202HL_95049.11Two base, cross-stacked hairpin loop
203HL_97971.11
204HL_13786.11
205HL_20806.11
206HL_30008.11
207HL_37962.11
208HL_46570.11
209HL_53789.11
210HL_57217.11cHS platform Intercalation Site
211HL_59604.11
212HL_78228.11
213HL_82243.11
214HL_84888.11T-loop like but without tWH UA
215HL_95716.11
216HL_03785.11LSU Helix 8 (H8) Hairpin Loop
217HL_10116.11Kink-turn-like Hairpin Loop
218HL_19132.11
219HL_26579.11
220HL_30128.11
221HL_42969.11
222HL_47337.11
223HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
224HL_59610.11
225HL_62970.11
226HL_65802.11
227HL_67761.11
228HL_70912.11
229HL_82288.11
230HL_85018.11
231HL_93263.11

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