Changes in PDB files used for clustering

Release 1.6 has 212 PDB files, release 1.7 has 213 PDB files, 212 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.7: 4KJI.

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

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Changes in motif groups

Release 1.6 has 249 motif groups, release 1.7 has 250 motif groups, 249 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.6, 1 groups are only in release 1.7.

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_72498.964T-loops with two bulged bases
3HL_39895.635UNCG Hairpin motifs
4HL_18781.420Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_97270.315T-loops with 1 bulged base
7HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_74465.212tRNA Anti-Codon loop
9HL_49036.312GNRA with one bulged base
10HL_48039.211MS2 virus RNA Hairpin
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_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_27271.110LSU Helix 96 (H96) Hairpin Loop
14HL_46175.21016S helix 23 and 24 hairpin loops
15HL_56824.210LSU Helix 60A. LSU Helix 63A.
16HL_68081.310LSU Helix 20 Hairpin loop
17HL_80459.39
18HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_82294.38SSU Helix 37 (h37) Hairpin loop.
23HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
24HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_57514.26Two base, cross-stacked hairpin loop
26HL_75579.26
27HL_41833.26LSU Helix 81 (H81) Hairpin Loop
28HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
29HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
30HL_87136.26LSU Helix 39A Hairpin loop
31HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
32HL_70420.26LSU Helix 97 Hairpin loop
33HL_18156.26LSU Helix 72 (H72) Hairpin Loop
34HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
35HL_42677.16
36HL_46489.26LSU H89 Hairpin Loop
37HL_39942.26LSU Helix 91 (H91) Hairpin Loop
38HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_06643.25tRNA D-loop. Sec tRNA
40HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_45018.35Hairpin-Hairpin Interacting HL
42HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
43HL_88311.25LSU Helix 35 (H35) Hairpin Loop
44HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
45HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
46HL_72273.15tRNA D-loop
47HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
48HL_11376.14LSU Helix 8 (H8) Hairpin Loop
49HL_47784.24SSU Central Pseudoknot (forms helix 2)
50HL_64543.24SSU Helix 31 (h31) Hairpin Loop
51HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
52HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
53HL_62881.14RNase P Structured Hairpin Loop
54HL_98523.24GNRA-like. Closed by tSH UC.
55HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
56HL_29831.14GNRA-like with bulged base.
57HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
58HL_41827.13
59HL_19221.23
60HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
61HL_68697.23
62HL_42077.23LSU Helix 28 (H28) Hairpin Loop
63HL_58083.23
64HL_61547.43
65HL_90579.23
66HL_23182.13
67HL_32644.13LSU Helix 69 (H69) Hairpin Loop
68HL_76036.33LSU Helix 8 (H8) Hairpin Loop
69HL_12595.23
70HL_25124.13tSW GA closed tetraloops
71HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
72HL_76766.23
73HL_27429.33
74HL_80492.23tRNA D-loop
75HL_08382.23
76HL_13707.23cSH AA Platform containing Hairpin Loop
77HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
78HL_74686.13SSU Central Pseudoknot (forms helix 2)
79HL_42687.33
80HL_78361.13
81HL_06122.12
82HL_21545.12LSU Helix 96 (H96) Hairpin Loop
83HL_24473.32tRNA D-loop
84HL_26143.12
85HL_38130.22
86HL_54751.22
87HL_60200.12
88HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
89HL_06312.12
90HL_16770.12
91HL_26495.12
92HL_64371.22
93HL_86398.12
94HL_90542.12
95HL_93771.12tRNA T-loop distorted by RS binding
96HL_99633.12
97HL_23129.12
98HL_50312.12
99HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
100HL_94578.12
101HL_06997.12
102HL_19399.12
103HL_24711.12
104HL_17790.12UNCG-like. cWW Closing pair.
105HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
106HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
107HL_84353.12
108HL_87554.12
109HL_91693.12
110HL_03791.12
111HL_19528.12
112HL_23290.12
113HL_42553.12
114HL_74559.12Two base, cross-stacked hairpin loop
115HL_91872.12
116HL_18587.12
117HL_33451.12
118HL_53753.12
119HL_62967.12
120HL_65924.12
121HL_81752.12
122HL_98577.12
123HL_05361.12
124HL_49210.12
125HL_75575.12
126HL_96915.12
127HL_98833.22
128HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
129HL_19132.11
130HL_30008.11
131HL_42969.11
132HL_47337.11
133HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
134HL_63304.11
135HL_66467.11
136HL_68579.11
137HL_78420.11
138HL_82288.11
139HL_90102.11Kink-turn-like Hairpin Loop
140HL_93633.11
141HL_96994.11
142HL_99207.11Tetrahymena LSU hairpin poorly modeled
143HL_00090.11
144HL_30128.11
145HL_38138.11
146HL_44390.11
147HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
148HL_55202.11U2B"-U2A" binding hairpin loop
149HL_57843.11
150HL_60203.11
151HL_66877.11cSH GU/cWS double platform, intercalation site
152HL_78507.11
153HL_01418.11
154HL_17537.11
155HL_19226.11
156HL_24707.11
157HL_26579.11
158HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
159HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
160HL_44522.11
161HL_55272.11
162HL_68733.11LSU Yeast Hairpin Loop
163HL_73465.11
164HL_75850.11
165HL_83865.11
166HL_97499.11
167HL_34440.11
168HL_39422.11
169HL_42345.11
170HL_52540.11
171HL_58223.11
172HL_65071.11
173HL_67000.11
174HL_69403.11GNRA-like
175HL_73972.11
176HL_79902.11
177HL_84289.11
178HL_87223.11
179HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
180HL_97784.11
181HL_03785.11LSU Helix 8 (H8) Hairpin Loop
182HL_07315.11
183HL_19452.11tRNA D-loop
184HL_23195.11
185HL_27397.11
186HL_33277.11
187HL_35200.11
188HL_39486.11
189HL_45411.11
190HL_56775.11
191HL_58601.11
192HL_62880.11
193HL_95049.11Two base, cross-stacked hairpin loop
194HL_97971.11
195HL_07915.11
196HL_12706.11
197HL_25175.11
198HL_35865.11
199HL_48480.11
200HL_53015.11
201HL_56809.11
202HL_59182.11
203HL_65802.11
204HL_67761.11
205HL_70912.11
206HL_77692.11tRNA D-loop
207HL_84888.11T-loop like but without tWH UA
208HL_95716.11
209HL_04194.11
210HL_25195.11
211HL_27819.11
212HL_36842.11
213HL_59604.11
214HL_71607.11
215HL_78228.11
216HL_85018.11
217HL_93530.11
218HL_10116.11Kink-turn-like Hairpin Loop
219HL_13786.11
220HL_20806.11
221HL_24108.11
222HL_25197.11
223HL_33640.11
224HL_37962.11
225HL_46570.11
226HL_53789.11
227HL_57217.11cHS platform Intercalation Site
228HL_59610.11
229HL_62970.11
230HL_68435.11
231HL_82243.11
232HL_88960.11
233HL_93567.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription
1HL_29196.11