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_46175.21016S helix 23 and 24 hairpin loops
10HL_68081.310LSU Helix 20 Hairpin loop
11HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_27271.110LSU Helix 96 (H96) Hairpin Loop
14HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
15HL_80459.39
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_15603.18U1A protein-binding Hairpin Loop.
18HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
19HL_34027.285S Loop C - Upper part of Hairpin Loop.
20HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_82294.38SSU Helix 37 (h37) Hairpin loop.
22HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
23HL_75579.26
24HL_87136.26LSU Helix 39A Hairpin loop
25HL_41833.26LSU Helix 81 (H81) Hairpin Loop
26HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
27HL_46489.26LSU H89 Hairpin Loop
28HL_39942.26LSU Helix 91 (H91) Hairpin Loop
29HL_57514.26Two base, cross-stacked hairpin loop
30HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
31HL_70420.26LSU Helix 97 Hairpin loop
32HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
33HL_18156.26LSU Helix 72 (H72) Hairpin Loop
34HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
35HL_72273.15tRNA D-loop
36HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
37HL_45018.35Hairpin-Hairpin Interacting HL
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
40HL_88311.25LSU Helix 35 (H35) Hairpin Loop
41HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
42HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
43HL_06643.25tRNA D-loop. Sec tRNA
44HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
45HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
46HL_64543.24SSU Helix 31 (h31) Hairpin Loop
47HL_62881.14RNase P Structured Hairpin Loop
48HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
49HL_47784.24SSU Central Pseudoknot (forms helix 2)
50HL_98523.24GNRA-like. Closed by tSH UC.
51HL_11376.14LSU Helix 8 (H8) Hairpin Loop
52HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
53HL_29831.14GNRA-like with bulged base.
54HL_58083.23
55HL_80492.23tRNA D-loop
56HL_27429.33
57HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
58HL_13707.23cSH AA Platform containing Hairpin Loop
59HL_23182.13
60HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
61HL_61547.43
62HL_08382.23
63HL_42077.23LSU Helix 28 (H28) Hairpin Loop
64HL_25124.13tSW GA closed tetraloops
65HL_68697.23
66HL_41827.13
67HL_19221.23
68HL_76036.33LSU Helix 8 (H8) Hairpin Loop
69HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
70HL_74686.13SSU Central Pseudoknot (forms helix 2)
71HL_78361.13
72HL_84353.12
73HL_17790.12UNCG-like. cWW Closing pair.
74HL_44467.12
75HL_18587.12
76HL_16770.12
77HL_38130.22
78HL_42553.12
79HL_19399.12
80HL_99633.12
81HL_33451.12
82HL_98577.12
83HL_21545.12LSU Helix 96 (H96) Hairpin Loop
84HL_96915.12
85HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
86HL_54751.22
87HL_94578.12
88HL_49210.12
89HL_19528.12
90HL_87554.12
91HL_86398.12
92HL_23290.12
93HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
94HL_64371.22
95HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
96HL_23129.12
97HL_91872.12
98HL_60200.12
99HL_90542.12
100HL_93771.12tRNA T-loop distorted by RS binding
101HL_65924.12
102HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
103HL_24711.12
104HL_24473.32tRNA D-loop
105HL_05361.12
106HL_74559.12Two base, cross-stacked hairpin loop
107HL_06122.12
108HL_91693.12
109HL_26495.12
110HL_50312.12
111HL_03791.12
112HL_62967.12
113HL_73972.11
114HL_24707.11
115HL_19226.11
116HL_45358.11Double hairpin loop based on GGA triple
117HL_42969.11
118HL_79902.11
119HL_30731.11
120HL_07915.11
121HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
122HL_75850.11
123HL_35200.11
124HL_82288.11
125HL_83865.11
126HL_01418.11
127HL_59182.11
128HL_59610.11
129HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
130HL_25197.11
131HL_93633.11
132HL_20806.11
133HL_68435.11
134HL_84888.11T-loop like but without tWH UA
135HL_57843.11
136HL_68579.11
137HL_27819.11
138HL_00090.11
139HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
140HL_39486.11
141HL_36842.11
142HL_23195.11
143HL_20028.11
144HL_29196.11
145HL_55202.11U2B"-U2A" binding hairpin loop
146HL_65802.11
147HL_35865.11
148HL_48480.11
149HL_78507.11
150HL_60203.11
151HL_58223.11
152HL_19132.11
153HL_12706.11
154HL_67761.11
155HL_63304.11
156HL_47337.11
157HL_33277.11
158HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
159HL_99584.11
160HL_38138.11
161HL_33640.11
162HL_30128.11
163HL_99779.11
164HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
165HL_87223.11
166HL_26579.11
167HL_58601.11
168HL_88960.11
169HL_91613.11
170HL_70912.11
171HL_13786.11
172HL_55272.11
173HL_78420.11
174HL_68733.11LSU Yeast Hairpin Loop
175HL_66467.11
176HL_99207.11Tetrahymena LSU hairpin poorly modeled
177HL_17537.11
178HL_08203.11
179HL_38898.11
180HL_93567.11
181HL_57923.11
182HL_97499.11
183HL_00721.11
184HL_44522.11
185HL_66877.11cSH GU/cWS double platform, intercalation site
186HL_53015.11
187HL_25175.11
188HL_90102.11Kink-turn-like Hairpin Loop
189HL_97784.11
190HL_85018.11
191HL_30008.11
192HL_17008.11Nova-2 KH3 domain binding hairpin
193HL_56775.11
194HL_45411.11
195HL_37962.11
196HL_65071.11
197HL_39422.11
198HL_66880.11
199HL_03785.11LSU Helix 8 (H8) Hairpin Loop
200HL_93530.11
201HL_19452.11tRNA D-loop
202HL_42345.11
203HL_77692.11tRNA D-loop
204HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
205HL_53789.11
206HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
207HL_57217.11cHS platform Intercalation Site
208HL_52540.11
209HL_84289.11
210HL_27397.11
211HL_44390.11
212HL_67000.11
213HL_62970.11
214HL_04194.11
215HL_95716.11
216HL_82243.11
217HL_10116.11Kink-turn-like Hairpin Loop
218HL_98233.11
219HL_96994.11
220HL_25195.11
221HL_59604.11
222HL_95049.11Two base, cross-stacked hairpin loop
223HL_05113.11
224HL_34440.11
225HL_56809.11
226HL_62880.11
227HL_78228.11
228HL_97971.11
229HL_69403.11GNRA-like
230HL_46570.11
231HL_73465.11
232HL_24108.11

Updated motif groups

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

Removed motif groups

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

Added motif groups

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