Changes in PDB files used for clustering

Release 1.8 has 217 PDB files, release 1.9 has 221 PDB files, 216 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_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
36HL_45018.35Hairpin-Hairpin Interacting HL
37HL_72273.15tRNA D-loop
38HL_88311.25LSU Helix 35 (H35) Hairpin Loop
39HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
40HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
41HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
42HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
43HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44HL_06643.25tRNA D-loop. Sec tRNA
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_68697.23
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_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
61HL_08382.23
62HL_90579.33LSU Helix 69 (H69) Hairpin Loop
63HL_76036.33LSU Helix 8 (H8) Hairpin Loop
64HL_19221.23
65HL_06997.23
66HL_13707.23cSH AA Platform containing Hairpin Loop
67HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
68HL_42687.43
69HL_58083.23
70HL_74686.13SSU Central Pseudoknot (forms helix 2)
71HL_27429.33
72HL_78361.13
73HL_63941.12
74HL_74505.12
75HL_38130.22
76HL_26495.12
77HL_42553.12
78HL_21545.12LSU Helix 96 (H96) Hairpin Loop
79HL_91872.12
80HL_93771.12tRNA T-loop distorted by RS binding
81HL_65249.12
82HL_33451.12
83HL_50312.12
84HL_19528.12
85HL_87554.12
86HL_60200.12
87HL_90542.12
88HL_06122.12
89HL_65924.12
90HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
91HL_32644.22LSU Helix 69 (H69) Hairpin Loop
92HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
93HL_23129.12
94HL_74559.12Two base, cross-stacked hairpin loop
95HL_84353.12
96HL_49210.12
97HL_94578.12
98HL_19399.12
99HL_98577.12
100HL_18587.12
101HL_62967.12
102HL_16770.12
103HL_23290.12
104HL_24711.12
105HL_24473.32tRNA D-loop
106HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
107HL_05361.12
108HL_64371.22
109HL_99633.12
110HL_91693.12
111HL_42094.12
112HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
113HL_54751.22
114HL_17790.12UNCG-like. cWW Closing pair.
115HL_76766.32
116HL_86398.12
117HL_96915.12
118HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
119HL_24707.11
120HL_28676.11
121HL_57217.11cHS platform Intercalation Site
122HL_52540.11
123HL_05113.11
124HL_79902.11
125HL_70912.11
126HL_03785.11LSU Helix 8 (H8) Hairpin Loop
127HL_25175.11
128HL_68733.11LSU Yeast Hairpin Loop
129HL_97784.11
130HL_85018.11
131HL_30008.11
132HL_84768.11
133HL_65802.11
134HL_35865.11
135HL_25197.11
136HL_20806.11
137HL_95049.11Two base, cross-stacked hairpin loop
138HL_42969.11
139HL_57843.11
140HL_62970.11
141HL_76679.11
142HL_90102.11Kink-turn-like Hairpin Loop
143HL_93530.11
144HL_19452.11tRNA D-loop
145HL_42345.11
146HL_38138.11
147HL_33640.11
148HL_48480.11
149HL_99779.11
150HL_19226.11
151HL_68435.11
152HL_84888.11T-loop like but without tWH UA
153HL_19132.11
154HL_62880.11
155HL_04194.11
156HL_95716.11
157HL_82243.11
158HL_10116.11Kink-turn-like Hairpin Loop
159HL_73465.11
160HL_96994.11
161HL_30128.11
162HL_78507.11
163HL_58223.11
164HL_88960.11
165HL_44390.11
166HL_67000.11
167HL_97971.11
168HL_69403.11GNRA-like
169HL_46570.11
170HL_01418.11
171HL_24108.11
172HL_56775.11
173HL_77692.11tRNA D-loop
174HL_93567.11
175HL_45411.11
176HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
177HL_60203.11
178HL_26579.11
179HL_58601.11
180HL_66877.11cSH GU/cWS double platform, intercalation site
181HL_56809.11
182HL_00090.11
183HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
184HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
185HL_78228.11
186HL_35200.11
187HL_82288.11
188HL_83865.11
189HL_20028.11
190HL_59182.11
191HL_59610.11
192HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
193HL_76585.11
194HL_87223.11
195HL_44522.11
196HL_27397.11
197HL_07915.11
198HL_67761.11
199HL_63304.11
200HL_75850.11
201HL_39486.11
202HL_36842.11
203HL_23195.11
204HL_59225.11
205HL_55202.11U2B"-U2A" binding hairpin loop
206HL_52116.11
207HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
208HL_25195.11
209HL_59604.11
210HL_97499.11
211HL_65071.11
212HL_39422.11
213HL_84289.11
214HL_34440.11
215HL_27819.11
216HL_13786.11
217HL_55272.11
218HL_47337.11
219HL_33277.11
220HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
221HL_99584.11
222HL_29196.11
223HL_73972.11
224HL_53789.11
225HL_37962.11
226HL_68579.11
227HL_12706.11
228HL_53015.11
229HL_78420.11
230HL_66467.11
231HL_99207.11Tetrahymena LSU hairpin poorly modeled
232HL_17537.11
233HL_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_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5HL_25124.24tSW GA closed tetraloops
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_93263.11
3HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking