Changes in PDB files used for clustering

Release 1.8 has 221 PDB files, release 1.9 has 225 PDB files, 220 of them are identical.

No equivalence class representatives have been replaced.

5 new structures in release 1.9: 4BW0, 4C7O, 4C9D, 4K27, 4LGT.

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 1.8 has 254 motif groups, release 1.9 has 253 motif groups, 243 of them are identical.

7 motif groups were updated, 4 groups are present only in release 1.8, 3 groups are only in release 1.9.

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_39895.635UNCG Hairpin motifs
2HL_18781.420Double sheared (tSH) with U-turn
3HL_91226.317Kissing Hairpin motif
4HL_97270.315T-loops with 1 bulged base
5HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_49036.312GNRA with one bulged base
7HL_48039.211MS2 virus RNA Hairpin
8HL_68081.310LSU Helix 20 Hairpin loop
9HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
10HL_56824.210LSU Helix 60A. LSU Helix 63A.
11HL_46175.21016S helix 23 and 24 hairpin loops
12HL_27271.110LSU Helix 96 (H96) Hairpin Loop
13HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_80459.39
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_82294.38SSU Helix 37 (h37) Hairpin loop.
17HL_34027.285S Loop C - Upper part of Hairpin Loop.
18HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
20HL_15603.18U1A protein-binding Hairpin Loop.
21HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_42677.27
23HL_41833.26LSU Helix 81 (H81) Hairpin Loop
24HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
25HL_46489.26LSU H89 Hairpin Loop
26HL_39942.26LSU Helix 91 (H91) Hairpin Loop
27HL_57514.26Two base, cross-stacked hairpin loop
28HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
29HL_70420.26LSU Helix 97 Hairpin loop
30HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
31HL_18156.26LSU Helix 72 (H72) Hairpin Loop
32HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
33HL_75579.26
34HL_87136.26LSU Helix 39A Hairpin loop
35HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
36HL_06643.25tRNA D-loop. Sec tRNA
37HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
38HL_45018.35Hairpin-Hairpin Interacting HL
39HL_72273.15tRNA D-loop
40HL_88311.25LSU Helix 35 (H35) Hairpin Loop
41HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
42HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
43HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
44HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
45HL_62881.14RNase P Structured Hairpin Loop
46HL_98523.24GNRA-like. Closed by tSH UC.
47HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
48HL_29831.14GNRA-like with bulged base.
49HL_11376.14LSU Helix 8 (H8) Hairpin Loop
50HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
51HL_47784.24SSU Central Pseudoknot (forms helix 2)
52HL_64543.24SSU Helix 31 (h31) Hairpin Loop
53HL_98833.33
54HL_27429.33
55HL_41827.13
56HL_23182.13
57HL_80492.23tRNA D-loop
58HL_42077.23LSU Helix 28 (H28) Hairpin Loop
59HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
60HL_78361.13
61HL_90579.33LSU Helix 69 (H69) Hairpin Loop
62HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
63HL_08382.23
64HL_19221.23
65HL_76036.33LSU Helix 8 (H8) Hairpin Loop
66HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
67HL_06997.23
68HL_13707.23cSH AA Platform containing Hairpin Loop
69HL_42687.43
70HL_58083.23
71HL_74686.13SSU Central Pseudoknot (forms helix 2)
72HL_68697.23
73HL_63941.12
74HL_74505.12
75HL_38130.22
76HL_26495.12
77HL_64371.22
78HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
79HL_23129.12
80HL_60200.12
81HL_90542.12
82HL_93771.12tRNA T-loop distorted by RS binding
83HL_65249.12
84HL_42553.12
85HL_76766.32
86HL_74559.12Two base, cross-stacked hairpin loop
87HL_06122.12
88HL_65924.12
89HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
90HL_33451.12
91HL_50312.12
92HL_44467.12
93HL_18587.12
94HL_62967.12
95HL_84353.12
96HL_49210.12
97HL_94578.12
98HL_32644.22LSU Helix 69 (H69) Hairpin Loop
99HL_16770.12
100HL_23290.12
101HL_19399.12
102HL_99633.12
103HL_24711.12
104HL_24473.32tRNA D-loop
105HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
106HL_21545.12LSU Helix 96 (H96) Hairpin Loop
107HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
108HL_91693.12
109HL_42094.12
110HL_05361.12
111HL_98577.12
112HL_86398.12
113HL_96915.12
114HL_54751.22
115HL_17790.12UNCG-like. cWW Closing pair.
116HL_19528.12
117HL_87554.12
118HL_91872.12
119HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
120HL_24707.11
121HL_37962.11
122HL_65071.11
123HL_44522.11
124HL_66880.11
125HL_62970.11
126HL_76679.11
127HL_90102.11Kink-turn-like Hairpin Loop
128HL_93530.11
129HL_19452.11tRNA D-loop
130HL_30008.11
131HL_84768.11
132HL_65802.11
133HL_35865.11
134HL_25197.11
135HL_28676.11
136HL_57217.11cHS platform Intercalation Site
137HL_39422.11
138HL_84289.11
139HL_27397.11
140HL_44390.11
141HL_67000.11
142HL_62880.11
143HL_04194.11
144HL_95716.11
145HL_82243.11
146HL_10116.11Kink-turn-like Hairpin Loop
147HL_98233.11
148HL_42345.11
149HL_38138.11
150HL_33640.11
151HL_48480.11
152HL_20806.11
153HL_52540.11
154HL_34440.11
155HL_56809.11
156HL_97971.11
157HL_69403.11GNRA-like
158HL_46570.11
159HL_73465.11
160HL_96994.11
161HL_30128.11
162HL_99779.11
163HL_19226.11
164HL_95049.11Two base, cross-stacked hairpin loop
165HL_05113.11
166HL_79902.11
167HL_30731.11
168HL_07915.11
169HL_00090.11
170HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
171HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
172HL_78228.11
173HL_35200.11
174HL_82288.11
175HL_83865.11
176HL_01418.11
177HL_24108.11
178HL_55202.11U2B"-U2A" binding hairpin loop
179HL_56775.11
180HL_77692.11tRNA D-loop
181HL_93567.11
182HL_57923.11
183HL_78507.11
184HL_45358.11Double hairpin loop based on GGA triple
185HL_42969.11
186HL_57843.11
187HL_68579.11
188HL_27819.11
189HL_67761.11
190HL_63304.11
191HL_75850.11
192HL_39486.11
193HL_36842.11
194HL_23195.11
195HL_20028.11
196HL_59182.11
197HL_59610.11
198HL_45411.11
199HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
200HL_60203.11
201HL_68435.11
202HL_84888.11T-loop like but without tWH UA
203HL_19132.11
204HL_12706.11
205HL_13786.11
206HL_55272.11
207HL_47337.11
208HL_33277.11
209HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
210HL_59225.11
211HL_38898.11
212HL_52116.11
213HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
214HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
215HL_76585.11
216HL_87223.11
217HL_58223.11
218HL_88960.11
219HL_91613.11
220HL_70912.11
221HL_53015.11
222HL_78420.11
223HL_66467.11
224HL_99207.11Tetrahymena LSU hairpin poorly modeled
225HL_17537.11
226HL_99584.11
227HL_29196.11
228HL_17008.11Nova-2 KH3 domain binding hairpin
229HL_73972.11
230HL_53789.11
231HL_25195.11
232HL_59604.11
233HL_97499.11
234HL_00721.11
235HL_26579.11
236HL_58601.11
237HL_66877.11cSH GU/cWS double platform, intercalation site
238HL_03785.11LSU Helix 8 (H8) Hairpin Loop
239HL_25175.11
240HL_68733.11LSU Yeast Hairpin Loop
241HL_97784.11
242HL_85018.11
243HL_08203.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.10229GNRA Hairpin motifs
2HL_72498.1165T-loops with two bulged bases
3HL_74465.412tRNA Anti-Codon loop
4HL_25124.24tSW GA closed tetraloops
5HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
6HL_35619.23
7HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking

Removed motif groups

#Motif idInstancesDescription
1HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
2HL_03791.12
3HL_93633.11
4HL_98234.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking

Added motif groups

#Motif idInstancesDescription
1HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
2HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
3HL_93263.11