Changes in PDB files used for clustering

Release 1.7 has 213 PDB files, release 1.8 has 216 PDB files, 213 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_27271.110LSU Helix 96 (H96) Hairpin Loop
10HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
11HL_46175.21016S helix 23 and 24 hairpin loops
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
14HL_56824.210LSU Helix 60A. LSU Helix 63A.
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_80459.39
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_15603.18U1A protein-binding Hairpin Loop.
19HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_82294.38SSU Helix 37 (h37) Hairpin loop.
23HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
24HL_70420.26LSU Helix 97 Hairpin loop
25HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
26HL_18156.26LSU Helix 72 (H72) Hairpin Loop
27HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28HL_75579.26
29HL_87136.26LSU Helix 39A Hairpin loop
30HL_41833.26LSU Helix 81 (H81) Hairpin Loop
31HL_57514.26Two base, cross-stacked hairpin loop
32HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
33HL_46489.26LSU H89 Hairpin Loop
34HL_39942.26LSU Helix 91 (H91) Hairpin Loop
35HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
36HL_88311.25LSU Helix 35 (H35) Hairpin Loop
37HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
38HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
39HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
41HL_72273.15tRNA D-loop
42HL_06643.25tRNA D-loop. Sec tRNA
43HL_45018.35Hairpin-Hairpin Interacting HL
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
45HL_29831.14GNRA-like with bulged base.
46HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
47HL_64543.24SSU Helix 31 (h31) Hairpin Loop
48HL_62881.14RNase P Structured Hairpin Loop
49HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
50HL_47784.24SSU Central Pseudoknot (forms helix 2)
51HL_98523.24GNRA-like. Closed by tSH UC.
52HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
53HL_11376.14LSU Helix 8 (H8) Hairpin Loop
54HL_41827.13
55HL_19221.23
56HL_27429.33
57HL_74686.13SSU Central Pseudoknot (forms helix 2)
58HL_25124.13tSW GA closed tetraloops
59HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
60HL_80492.23tRNA D-loop
61HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
62HL_58083.23
63HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
64HL_78361.13
65HL_13707.23cSH AA Platform containing Hairpin Loop
66HL_23182.13
67HL_76036.33LSU Helix 8 (H8) Hairpin Loop
68HL_68697.23
69HL_61547.43
70HL_08382.23
71HL_42077.23LSU Helix 28 (H28) Hairpin Loop
72HL_23290.12
73HL_62967.12
74HL_93771.12tRNA T-loop distorted by RS binding
75HL_65924.12
76HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
77HL_24711.12
78HL_24473.32tRNA D-loop
79HL_26495.12
80HL_19399.12
81HL_03791.12
82HL_18587.12
83HL_06122.12
84HL_91693.12
85HL_42553.12
86HL_64371.22
87HL_99633.12
88HL_84353.12
89HL_17790.12UNCG-like. cWW Closing pair.
90HL_33451.12
91HL_96915.12
92HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
93HL_16770.12
94HL_38130.22
95HL_94578.12
96HL_21545.12LSU Helix 96 (H96) Hairpin Loop
97HL_86398.12
98HL_54751.22
99HL_19528.12
100HL_87554.12
101HL_91872.12
102HL_60200.12
103HL_90542.12
104HL_49210.12
105HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
106HL_05361.12
107HL_50312.12
108HL_98577.12
109HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
110HL_23129.12
111HL_74559.12Two base, cross-stacked hairpin loop
112HL_56775.11
113HL_53789.11
114HL_25195.11
115HL_19226.11
116HL_58223.11
117HL_58601.11
118HL_88960.11
119HL_44390.11
120HL_67000.11
121HL_62880.11
122HL_78228.11
123HL_97971.11
124HL_69403.11GNRA-like
125HL_46570.11
126HL_01418.11
127HL_77692.11tRNA D-loop
128HL_20806.11
129HL_26579.11
130HL_66877.11cSH GU/cWS double platform, intercalation site
131HL_56809.11
132HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
133HL_75850.11
134HL_35200.11
135HL_82288.11
136HL_83865.11
137HL_30008.11
138HL_24707.11
139HL_78507.11
140HL_60203.11
141HL_44522.11
142HL_27397.11
143HL_07915.11
144HL_00090.11
145HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
146HL_39486.11
147HL_36842.11
148HL_23195.11
149HL_42345.11
150HL_73972.11
151HL_25197.11
152HL_93633.11
153HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
154HL_87223.11
155HL_39422.11
156HL_84289.11
157HL_34440.11
158HL_27819.11
159HL_67761.11
160HL_63304.11
161HL_47337.11
162HL_33277.11
163HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
164HL_96994.11
165HL_59610.11
166HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
167HL_48480.11
168HL_97499.11
169HL_65071.11
170HL_68579.11
171HL_12706.11
172HL_13786.11
173HL_55272.11
174HL_78420.11
175HL_68733.11LSU Yeast Hairpin Loop
176HL_66467.11
177HL_99207.11Tetrahymena LSU hairpin poorly modeled
178HL_17537.11
179HL_24108.11
180HL_65802.11
181HL_35865.11
182HL_30128.11
183HL_37962.11
184HL_52540.11
185HL_42969.11
186HL_79902.11
187HL_70912.11
188HL_53015.11
189HL_25175.11
190HL_90102.11Kink-turn-like Hairpin Loop
191HL_97784.11
192HL_85018.11
193HL_59182.11
194HL_38138.11
195HL_33640.11
196HL_93567.11
197HL_45411.11
198HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
199HL_57217.11cHS platform Intercalation Site
200HL_95049.11Two base, cross-stacked hairpin loop
201HL_84888.11T-loop like but without tWH UA
202HL_57843.11
203HL_03785.11LSU Helix 8 (H8) Hairpin Loop
204HL_93530.11
205HL_19452.11tRNA D-loop
206HL_29196.11
207HL_55202.11U2B"-U2A" binding hairpin loop
208HL_59604.11
209HL_68435.11
210HL_19132.11
211HL_62970.11
212HL_04194.11
213HL_95716.11
214HL_82243.11
215HL_10116.11Kink-turn-like Hairpin Loop
216HL_73465.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.1066T-loops with two bulged bases
2HL_74465.313tRNA Anti-Codon loop
3HL_42677.27
4HL_21675.23LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5HL_98833.33
6HL_42687.43
7HL_06997.23
8HL_90579.33LSU Helix 69 (H69) Hairpin Loop
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_07315.11
8HL_71607.11

Added motif groups

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