Changes in PDB files used for clustering

Release 1.13 has 231 PDB files, release 1.14 has 236 PDB files, 230 of them are identical.

1 equivalence classes changed representatives: 3V2F4NVV.

5 new structures in release 1.14: 1VW3, 1VW4, 4KR6, 4KR7, 4OOG.

Obsolete: 3V2F4V8I.

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 1.13 has 253 motif groups, release 1.14 has 264 motif groups, 181 of them are identical.

45 motif groups were updated, 27 groups are present only in release 1.13, 38 groups are only in release 1.14.

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_74465.513tRNA Anti-Codon loop
2HL_27271.212LSU Helix 96 (H96) Hairpin Loop
3HL_48039.211MS2 virus RNA Hairpin
4HL_15603.29U1A protein-binding Hairpin Loop.
5HL_82294.38SSU Helix 37 (h37) Hairpin loop.
6HL_42677.27
7HL_06643.36tRNA D-loop. Sec tRNA
8HL_57514.26Two base, cross-stacked hairpin loop
9HL_45018.35Hairpin-Hairpin Interacting HL
10HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
11HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
12HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
13HL_72273.15tRNA D-loop
14HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
15HL_64543.24SSU Helix 31 (h31) Hairpin Loop
16HL_62881.14RNase P Structured Hairpin Loop
17HL_98523.24GNRA-like. Closed by tSH UC.
18HL_25124.24tSW GA closed tetraloops
19HL_86115.14
20HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
21HL_11376.14LSU Helix 8 (H8) Hairpin Loop
22HL_13707.23cSH AA Platform containing Hairpin Loop
23HL_06997.23
24HL_19221.23
25HL_98833.33
26HL_23182.13
27HL_78361.13
28HL_41827.13
29HL_80492.23tRNA D-loop
30HL_76766.43
31HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
32HL_58083.23
33HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
34HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
35HL_98577.12
36HL_44467.12
37HL_18587.12
38HL_42094.12
39HL_05361.12
40HL_99633.12
41HL_96915.12
42HL_54751.22
43HL_49210.12
44HL_93771.12tRNA T-loop distorted by RS binding
45HL_23290.12
46HL_26495.12
47HL_42553.12
48HL_90542.12
49HL_06122.12
50HL_24473.32tRNA D-loop
51HL_33451.12
52HL_87554.12
53HL_86398.12
54HL_74505.12
55HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
56HL_17790.12UNCG-like. cWW Closing pair.
57HL_50312.12
58HL_23129.12
59HL_91872.12
60HL_60200.12
61HL_38130.22
62HL_94578.12
63HL_19528.12
64HL_74559.12Two base, cross-stacked hairpin loop
65HL_65924.12
66HL_24711.12
67HL_65249.12
68HL_19399.12
69HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
70HL_62967.12
71HL_38898.11
72HL_59610.11
73HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
74HL_35865.11
75HL_45411.11
76HL_20806.11
77HL_60203.11
78HL_68435.11
79HL_66877.11cSH GU/cWS double platform, intercalation site
80HL_44390.11
81HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
82HL_75850.11
83HL_82288.11
84HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
85HL_20028.11
86HL_59182.11
87HL_17008.11Nova-2 KH3 domain binding hairpin
88HL_33640.11
89HL_78507.11
90HL_87223.11
91HL_58223.11
92HL_66880.11
93HL_56809.11
94HL_00090.11
95HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
96HL_99207.11Tetrahymena LSU hairpin poorly modeled
97HL_17537.11
98HL_59225.11
99HL_53789.11
100HL_25195.11
101HL_97499.11
102HL_00721.11
103HL_26579.11
104HL_84289.11
105HL_27397.11
106HL_12706.11
107HL_67761.11
108HL_63304.11
109HL_47337.11
110HL_68733.11LSU Yeast Hairpin Loop
111HL_97784.11
112HL_85018.11
113HL_99584.11
114HL_29196.11
115HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
116HL_37962.11
117HL_65071.11
118HL_44522.11
119HL_30731.11
120HL_70912.11
121HL_13786.11
122HL_55272.11
123HL_78420.11
124HL_90102.11Kink-turn-like Hairpin Loop
125HL_19452.11tRNA D-loop
126HL_08203.11
127HL_20920.11
128HL_84768.11
129HL_77692.11tRNA D-loop
130HL_65802.11
131HL_24707.11
132HL_57217.11cHS platform Intercalation Site
133HL_39422.11
134HL_79902.11
135HL_68579.11
136HL_53015.11
137HL_25175.11
138HL_95716.11
139HL_10116.11Kink-turn-like Hairpin Loop
140HL_98233.11
141HL_30008.11
142HL_38138.11
143HL_25197.11
144HL_48480.11
145HL_99779.11
146HL_52540.11
147HL_57843.11
148HL_91613.11
149HL_03785.11LSU Helix 8 (H8) Hairpin Loop
150HL_93530.11
151HL_46570.11
152HL_73465.11
153HL_42345.11
154HL_56775.11
155HL_52116.11
156HL_19226.11
157HL_95049.11Two base, cross-stacked hairpin loop
158HL_05113.11
159HL_19132.11
160HL_67000.11
161HL_62970.11
162HL_04194.11
163HL_82243.11
164HL_83865.11
165HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
166HL_96994.11
167HL_55202.11U2B"-U2A" binding hairpin loop
168HL_73972.11
169HL_93567.11
170HL_57923.11
171HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
172HL_45358.11Double hairpin loop based on GGA triple
173HL_84888.11T-loop like but without tWH UA
174HL_88960.11
175HL_93263.11
176HL_62880.11
177HL_78228.11
178HL_69403.11GNRA-like
179HL_23195.11
180HL_01418.11
181HL_24108.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.13238GNRA Hairpin motifs
2HL_72498.1367T-loops with two bulged bases
3HL_39895.735UNCG Hairpin motifs
4HL_18781.521Double sheared (tSH) with U-turn
5HL_91226.417Kissing Hairpin motif
6HL_97270.415T-loops with 1 bulged base
7HL_52574.415LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_49036.412LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
9HL_56824.311LSU Helix 60A. LSU Helix 63A.
10HL_46175.31116S helix 23 and 24 hairpin loops
11HL_75759.510
12HL_17723.510LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_68081.410LSU Helix 20 Hairpin loop
14HL_33402.49LSU Helix 13 (H13) Hairpin loop. GNRA-like.
15HL_80459.49
16HL_11547.38LSU Helix 80 (H80) P-site Hairpin Loop.
17HL_34027.385S Loop C - Upper part of Hairpin Loop.
18HL_24544.38LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19HL_87844.38LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
20HL_41833.37LSU Helix 81 (H81) Hairpin Loop
21HL_34108.37LSU Helix 37 (H37) Hairpin Loop.
22HL_46489.37LSU H89 Hairpin Loop
23HL_18156.37LSU Helix 72 (H72) Hairpin Loop
24HL_39872.37LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25HL_70420.37LSU Helix 97 Hairpin loop
26HL_87136.37LSU Helix 39A Hairpin loop
27HL_01926.47LSU Helix 71 (H71) Hairpin Loop.
28HL_39942.37LSU Helix 91 (H91) Hairpin Loop
29HL_75579.36
30HL_88311.36LSU Helix 35 (H35) Hairpin Loop
31HL_11509.36LSU Helix 6 (H6) Hairpin Loop.
32HL_62228.46LSU Helix 35A (H35A) Hairpin Loop
33HL_85534.26LSU Helix 65 (H65) Hairpin Loop. T-loop like.
34HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
35HL_82538.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
36HL_08382.34
37HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
38HL_27429.43
39HL_64371.33SSU Central Pseudoknot (forms helix 2)
40HL_91693.23
41HL_35619.33
42HL_48254.23LSU Helix 84 (H84) Hairpin Loop.
43HL_68697.33
44HL_21545.23LSU Helix 96 (H96) Hairpin Loop
45HL_42077.32LSU Helix 28 (H28) Hairpin Loop

Removed motif groups

#Motif idInstancesDescription
1HL_29831.14GNRA-like with bulged base.
2HL_47784.24SSU Central Pseudoknot (forms helix 2)
3HL_74686.13SSU Central Pseudoknot (forms helix 2)
4HL_76036.33LSU Helix 8 (H8) Hairpin Loop
5HL_90579.33LSU Helix 69 (H69) Hairpin Loop
6HL_16770.12
7HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
9HL_32644.22LSU Helix 69 (H69) Hairpin Loop
10HL_84353.12
11HL_63941.12
12HL_35200.11
13HL_66467.11
14HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
15HL_36842.11
16HL_97971.11
17HL_28676.11
18HL_39486.11
19HL_42969.11
20HL_30128.11
21HL_76585.11
22HL_58601.11
23HL_76679.11
24HL_33277.11
25HL_59604.11
26HL_07915.11
27HL_34440.11

Added motif groups

#Motif idInstancesDescription
1HL_89236.16LSU Helix 69 (H69) Hairpin Loop
2HL_86077.15GNRA with one bulged base | GNRA-like with bulged base.
3HL_31318.15SSU Central Pseudoknot (forms helix 2)
4HL_99908.14LSU Helix 69 (H69) Hairpin Loop
5HL_82418.14LSU Helix 8 (H8) Hairpin Loop
6HL_16643.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
7HL_79956.13GNRA-like with 5'-stacking of first unpaired base.
8HL_84258.13LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
9HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
10HL_46903.12
11HL_78660.12
12HL_86889.12SSU Central Pseudoknot (forms helix 2)
13HL_16728.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
14HL_81510.12LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
15HL_92635.12
16HL_50461.12
17HL_94309.12GNRA with one bulged base
18HL_53745.12
19HL_95756.12
20HL_10075.11
21HL_59982.11
22HL_85982.11
23HL_96012.11
24HL_10894.11
25HL_46055.11
26HL_63997.11
27HL_97022.11
28HL_99612.11
29HL_49998.11
30HL_19363.11
31HL_50018.11
32HL_99932.11
33HL_23080.11
34HL_93428.11
35HL_27236.11
36HL_53116.11
37HL_82622.11SSU Central Pseudoknot (forms helix 2)
38HL_04305.11