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_49036.312GNRA with one bulged base
9HL_74465.212tRNA Anti-Codon loop
10HL_48039.211MS2 virus RNA Hairpin
11HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_46175.21016S helix 23 and 24 hairpin loops
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_56824.210LSU Helix 60A. LSU Helix 63A.
16HL_27271.110LSU Helix 96 (H96) Hairpin Loop
17HL_80459.39
18HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23HL_15603.18U1A protein-binding Hairpin Loop.
24HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
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_42677.16
29HL_75579.26
30HL_87136.26LSU Helix 39A Hairpin loop
31HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
32HL_41833.26LSU Helix 81 (H81) Hairpin Loop
33HL_46489.26LSU H89 Hairpin Loop
34HL_57514.26Two base, cross-stacked hairpin loop
35HL_39942.26LSU Helix 91 (H91) Hairpin Loop
36HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
37HL_70420.26LSU Helix 97 Hairpin loop
38HL_06643.25tRNA D-loop. Sec tRNA
39HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_72273.15tRNA D-loop
41HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42HL_45018.35Hairpin-Hairpin Interacting HL
43HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
44HL_88311.25LSU Helix 35 (H35) Hairpin Loop
45HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
46HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
47HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
48HL_62881.14RNase P Structured Hairpin Loop
49HL_29831.14GNRA-like with bulged base.
50HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
51HL_11376.14LSU Helix 8 (H8) Hairpin Loop
52HL_98523.24GNRA-like. Closed by tSH UC.
53HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
54HL_47784.24SSU Central Pseudoknot (forms helix 2)
55HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
56HL_64543.24SSU Helix 31 (h31) Hairpin Loop
57HL_42687.33
58HL_74686.13SSU Central Pseudoknot (forms helix 2)
59HL_27429.33
60HL_76766.23
61HL_78361.13
62HL_41827.13
63HL_58083.23
64HL_61547.43
65HL_80492.23tRNA D-loop
66HL_68697.23
67HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
68HL_08382.23
69HL_42077.23LSU Helix 28 (H28) Hairpin Loop
70HL_23182.13
71HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
72HL_32644.13LSU Helix 69 (H69) Hairpin Loop
73HL_76036.33LSU Helix 8 (H8) Hairpin Loop
74HL_25124.13tSW GA closed tetraloops
75HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
76HL_90579.23
77HL_13707.23cSH AA Platform containing Hairpin Loop
78HL_12595.23
79HL_19221.23
80HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
81HL_93771.12tRNA T-loop distorted by RS binding
82HL_53753.12
83HL_96915.12
84HL_06122.12
85HL_98833.22
86HL_17790.12UNCG-like. cWW Closing pair.
87HL_26495.12
88HL_06312.12
89HL_21545.12LSU Helix 96 (H96) Hairpin Loop
90HL_86398.12
91HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
92HL_84353.12
93HL_65924.12
94HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
95HL_38130.22
96HL_42553.12
97HL_50312.12
98HL_19528.12
99HL_87554.12
100HL_91872.12
101HL_16770.12
102HL_75575.12
103HL_33451.12
104HL_98577.12
105HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
106HL_23129.12
107HL_26143.12
108HL_60200.12
109HL_19399.12
110HL_74559.12Two base, cross-stacked hairpin loop
111HL_90542.12
112HL_06997.12
113HL_24711.12
114HL_49210.12
115HL_94578.12
116HL_03791.12
117HL_18587.12
118HL_62967.12
119HL_81752.12
120HL_91693.12
121HL_23290.12
122HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
123HL_64371.22
124HL_54751.22
125HL_24473.32tRNA D-loop
126HL_05361.12
127HL_99633.12
128HL_73972.11
129HL_53789.11
130HL_25195.11
131HL_37962.11
132HL_68579.11
133HL_12706.11
134HL_13786.11
135HL_55272.11
136HL_47337.11
137HL_33277.11
138HL_36842.11
139HL_23195.11
140HL_42345.11
141HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
142HL_24707.11
143HL_57217.11cHS platform Intercalation Site
144HL_52540.11
145HL_42969.11
146HL_79902.11
147HL_70912.11
148HL_53015.11
149HL_78420.11
150HL_68733.11LSU Yeast Hairpin Loop
151HL_66467.11
152HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
153HL_96994.11
154HL_38138.11
155HL_25197.11
156HL_20806.11
157HL_95049.11Two base, cross-stacked hairpin loop
158HL_84888.11T-loop like but without tWH UA
159HL_57843.11
160HL_03785.11LSU Helix 8 (H8) Hairpin Loop
161HL_25175.11
162HL_90102.11Kink-turn-like Hairpin Loop
163HL_99207.11Tetrahymena LSU hairpin poorly modeled
164HL_17537.11
165HL_24108.11
166HL_33640.11
167HL_65802.11
168HL_35865.11
169HL_93633.11
170HL_19226.11
171HL_68435.11
172HL_19132.11
173HL_62970.11
174HL_93530.11
175HL_97784.11
176HL_85018.11
177HL_59182.11
178HL_55202.11U2B"-U2A" binding hairpin loop
179HL_56775.11
180HL_30128.11
181HL_48480.11
182HL_78507.11
183HL_58223.11
184HL_58601.11
185HL_88960.11
186HL_44390.11
187HL_67000.11
188HL_62880.11
189HL_04194.11
190HL_95716.11
191HL_71607.11
192HL_19452.11tRNA D-loop
193HL_59610.11
194HL_77692.11tRNA D-loop
195HL_93567.11
196HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
197HL_60203.11
198HL_26579.11
199HL_66877.11cSH GU/cWS double platform, intercalation site
200HL_56809.11
201HL_78228.11
202HL_97971.11
203HL_82243.11
204HL_10116.11Kink-turn-like Hairpin Loop
205HL_73465.11
206HL_45411.11
207HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
208HL_87223.11
209HL_44522.11
210HL_27397.11
211HL_07915.11
212HL_00090.11
213HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
214HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
215HL_75850.11
216HL_35200.11
217HL_69403.11GNRA-like
218HL_46570.11
219HL_01418.11
220HL_07315.11
221HL_59604.11
222HL_97499.11
223HL_65071.11
224HL_39422.11
225HL_84289.11
226HL_34440.11
227HL_27819.11
228HL_67761.11
229HL_63304.11
230HL_39486.11
231HL_82288.11
232HL_83865.11
233HL_30008.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription
1HL_29196.11