Changes in PDB files used for clustering

Release 1.7 has 218 PDB files, release 1.8 has 221 PDB files, 218 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.8: 4L8H, 4MGM, 4MGN.

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 1.7 has 250 motif groups, release 1.8 has 254 motif groups, 232 of them are identical.

10 motif groups were updated, 8 groups are present only in release 1.7, 12 groups are only in release 1.8.

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_67042.9226GNRA 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_56824.210LSU Helix 60A. LSU Helix 63A.
10HL_27271.110LSU Helix 96 (H96) Hairpin Loop
11HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_46175.21016S helix 23 and 24 hairpin loops
13HL_68081.310LSU Helix 20 Hairpin loop
14HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_80459.39
17HL_82294.38SSU Helix 37 (h37) Hairpin loop.
18HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23HL_39942.26LSU Helix 91 (H91) Hairpin Loop
24HL_57514.26Two base, cross-stacked hairpin loop
25HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
26HL_70420.26LSU Helix 97 Hairpin loop
27HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
28HL_18156.26LSU Helix 72 (H72) Hairpin Loop
29HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_75579.26
31HL_87136.26LSU Helix 39A Hairpin loop
32HL_41833.26LSU Helix 81 (H81) Hairpin Loop
33HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
34HL_46489.26LSU H89 Hairpin Loop
35HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
36HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
37HL_88311.25LSU Helix 35 (H35) Hairpin Loop
38HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
39HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
40HL_06643.25tRNA D-loop. Sec tRNA
41HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
42HL_72273.15tRNA D-loop
43HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44HL_45018.35Hairpin-Hairpin Interacting HL
45HL_11376.14LSU Helix 8 (H8) Hairpin Loop
46HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
47HL_29831.14GNRA-like with bulged base.
48HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
49HL_64543.24SSU Helix 31 (h31) Hairpin Loop
50HL_62881.14RNase P Structured Hairpin Loop
51HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
52HL_47784.24SSU Central Pseudoknot (forms helix 2)
53HL_98523.24GNRA-like. Closed by tSH UC.
54HL_08382.23
55HL_42077.23LSU Helix 28 (H28) Hairpin Loop
56HL_25124.13tSW GA closed tetraloops
57HL_68697.23
58HL_41827.13
59HL_19221.23
60HL_76036.33LSU Helix 8 (H8) Hairpin Loop
61HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
62HL_74686.13SSU Central Pseudoknot (forms helix 2)
63HL_78361.13
64HL_58083.23
65HL_80492.23tRNA D-loop
66HL_27429.33
67HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
68HL_13707.23cSH AA Platform containing Hairpin Loop
69HL_23182.13
70HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
71HL_61547.43
72HL_49210.12
73HL_19528.12
74HL_87554.12
75HL_86398.12
76HL_23290.12
77HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
78HL_64371.22
79HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
80HL_23129.12
81HL_91872.12
82HL_60200.12
83HL_90542.12
84HL_93771.12tRNA T-loop distorted by RS binding
85HL_65924.12
86HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
87HL_24711.12
88HL_24473.32tRNA D-loop
89HL_05361.12
90HL_74559.12Two base, cross-stacked hairpin loop
91HL_06122.12
92HL_91693.12
93HL_26495.12
94HL_50312.12
95HL_03791.12
96HL_62967.12
97HL_84353.12
98HL_17790.12UNCG-like. cWW Closing pair.
99HL_44467.12
100HL_18587.12
101HL_16770.12
102HL_38130.22
103HL_42553.12
104HL_19399.12
105HL_99633.12
106HL_33451.12
107HL_98577.12
108HL_21545.12LSU Helix 96 (H96) Hairpin Loop
109HL_96915.12
110HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
111HL_54751.22
112HL_94578.12
113HL_38898.11
114HL_93567.11
115HL_57923.11
116HL_97499.11
117HL_00721.11
118HL_44522.11
119HL_66877.11cSH GU/cWS double platform, intercalation site
120HL_53015.11
121HL_25175.11
122HL_90102.11Kink-turn-like Hairpin Loop
123HL_97784.11
124HL_85018.11
125HL_30008.11
126HL_17008.11Nova-2 KH3 domain binding hairpin
127HL_56775.11
128HL_45411.11
129HL_37962.11
130HL_65071.11
131HL_39422.11
132HL_66880.11
133HL_03785.11LSU Helix 8 (H8) Hairpin Loop
134HL_93530.11
135HL_19452.11tRNA D-loop
136HL_42345.11
137HL_77692.11tRNA D-loop
138HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
139HL_53789.11
140HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
141HL_57217.11cHS platform Intercalation Site
142HL_52540.11
143HL_84289.11
144HL_27397.11
145HL_44390.11
146HL_67000.11
147HL_62970.11
148HL_04194.11
149HL_95716.11
150HL_82243.11
151HL_10116.11Kink-turn-like Hairpin Loop
152HL_98233.11
153HL_96994.11
154HL_25195.11
155HL_59604.11
156HL_95049.11Two base, cross-stacked hairpin loop
157HL_05113.11
158HL_34440.11
159HL_56809.11
160HL_62880.11
161HL_78228.11
162HL_97971.11
163HL_69403.11GNRA-like
164HL_46570.11
165HL_73465.11
166HL_24108.11
167HL_73972.11
168HL_24707.11
169HL_19226.11
170HL_45358.11Double hairpin loop based on GGA triple
171HL_42969.11
172HL_79902.11
173HL_30731.11
174HL_07915.11
175HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
176HL_75850.11
177HL_35200.11
178HL_82288.11
179HL_83865.11
180HL_01418.11
181HL_59182.11
182HL_59610.11
183HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
184HL_25197.11
185HL_93633.11
186HL_20806.11
187HL_68435.11
188HL_84888.11T-loop like but without tWH UA
189HL_57843.11
190HL_68579.11
191HL_27819.11
192HL_00090.11
193HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
194HL_39486.11
195HL_36842.11
196HL_23195.11
197HL_20028.11
198HL_29196.11
199HL_55202.11U2B"-U2A" binding hairpin loop
200HL_65802.11
201HL_35865.11
202HL_48480.11
203HL_78507.11
204HL_60203.11
205HL_58223.11
206HL_19132.11
207HL_12706.11
208HL_67761.11
209HL_63304.11
210HL_47337.11
211HL_33277.11
212HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
213HL_99584.11
214HL_38138.11
215HL_33640.11
216HL_30128.11
217HL_99779.11
218HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
219HL_87223.11
220HL_26579.11
221HL_58601.11
222HL_88960.11
223HL_91613.11
224HL_70912.11
225HL_13786.11
226HL_55272.11
227HL_78420.11
228HL_68733.11LSU Yeast Hairpin Loop
229HL_66467.11
230HL_99207.11Tetrahymena LSU hairpin poorly modeled
231HL_17537.11
232HL_08203.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.1066T-loops with two bulged bases
2HL_74465.313tRNA Anti-Codon loop
3HL_42677.27
4HL_42687.43
5HL_06997.23
6HL_90579.33LSU Helix 69 (H69) Hairpin Loop
7HL_21675.23LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8HL_98833.33
9HL_32644.22LSU Helix 69 (H69) Hairpin Loop
10HL_76766.32

Removed motif groups

#Motif idInstancesDescription
1HL_12595.23
2HL_26143.12
3HL_53753.12
4HL_75575.12
5HL_81752.12
6HL_06312.12
7HL_71607.11
8HL_07315.11

Added motif groups

#Motif idInstancesDescription
1HL_35619.13
2HL_42094.12
3HL_63941.12
4HL_65249.12
5HL_74505.12
6HL_84768.11
7HL_52116.11
8HL_98234.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
9HL_59225.11
10HL_28676.11
11HL_76585.11
12HL_76679.11