Changes in PDB files used for clustering

Release 1.13 has 226 PDB files, release 1.14 has 230 PDB files, 225 of them are identical.

1 equivalence classes changed representatives: 3V2F4NVV.

4 new structures in release 1.14: 1VW3, 1VW4, 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_57514.26Two base, cross-stacked hairpin loop
8HL_06643.36tRNA D-loop. Sec tRNA
9HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
10HL_45018.35Hairpin-Hairpin Interacting HL
11HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
12HL_72273.15tRNA D-loop
13HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
14HL_64543.24SSU Helix 31 (h31) Hairpin Loop
15HL_25124.24tSW GA closed tetraloops
16HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
17HL_62881.14RNase P Structured Hairpin Loop
18HL_98523.24GNRA-like. Closed by tSH UC.
19HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
20HL_86115.14
21HL_11376.14LSU Helix 8 (H8) Hairpin Loop
22HL_19221.23
23HL_13707.23cSH AA Platform containing Hairpin Loop
24HL_23182.13
25HL_78361.13
26HL_58083.23
27HL_06997.23
28HL_41827.13
29HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
30HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
31HL_80492.23tRNA D-loop
32HL_98833.33
33HL_76766.43
34HL_42553.12
35HL_60200.12
36HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
37HL_96915.12
38HL_99633.12
39HL_23129.12
40HL_38130.22
41HL_86398.12
42HL_05361.12
43HL_49210.12
44HL_54751.22
45HL_65249.12
46HL_06122.12
47HL_19399.12
48HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
49HL_87554.12
50HL_93771.12tRNA T-loop distorted by RS binding
51HL_23290.12
52HL_33451.12
53HL_74505.12
54HL_94578.12
55HL_19528.12
56HL_26495.12
57HL_50312.12
58HL_62967.12
59HL_65924.12
60HL_74559.12Two base, cross-stacked hairpin loop
61HL_98577.12
62HL_17790.12UNCG-like. cWW Closing pair.
63HL_24473.32tRNA D-loop
64HL_42094.12
65HL_90542.12
66HL_18587.12
67HL_91872.12
68HL_24711.12
69HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
70HL_53015.11
71HL_57217.11cHS platform Intercalation Site
72HL_67000.11
73HL_77692.11tRNA D-loop
74HL_82288.11
75HL_93263.11
76HL_04194.11
77HL_12706.11
78HL_29196.11
79HL_48480.11
80HL_53789.11
81HL_60203.11
82HL_65071.11
83HL_67761.11
84HL_73465.11
85HL_78228.11
86HL_93530.11
87HL_96994.11
88HL_19226.11
89HL_25175.11
90HL_30008.11
91HL_38138.11
92HL_44390.11
93HL_57843.11
94HL_68435.11
95HL_73972.11
96HL_83865.11
97HL_87223.11
98HL_93567.11
99HL_97499.11
100HL_13786.11
101HL_23195.11
102HL_25195.11
103HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
104HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
105HL_44522.11
106HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
107HL_55202.11U2B"-U2A" binding hairpin loop
108HL_62880.11
109HL_68579.11
110HL_78420.11
111HL_84289.11
112HL_97784.11
113HL_19452.11tRNA D-loop
114HL_25197.11
115HL_39422.11
116HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
117HL_55272.11
118HL_58223.11
119HL_65802.11
120HL_68733.11LSU Yeast Hairpin Loop
121HL_78507.11
122HL_84768.11
123HL_88960.11
124HL_17537.11
125HL_24108.11
126HL_33640.11
127HL_45411.11
128HL_59182.11
129HL_69403.11GNRA-like
130HL_79902.11
131HL_84888.11T-loop like but without tWH UA
132HL_90102.11Kink-turn-like Hairpin Loop
133HL_95049.11Two base, cross-stacked hairpin loop
134HL_00090.11
135HL_10116.11Kink-turn-like Hairpin Loop
136HL_26579.11
137HL_46570.11
138HL_52116.11
139HL_56775.11
140HL_59225.11
141HL_62970.11
142HL_70912.11
143HL_75850.11
144HL_85018.11
145HL_95716.11
146HL_01418.11
147HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
148HL_20806.11
149HL_24707.11
150HL_35865.11
151HL_42345.11
152HL_47337.11
153HL_52540.11
154HL_56809.11
155HL_59610.11
156HL_63304.11
157HL_66877.11cSH GU/cWS double platform, intercalation site
158HL_82243.11
159HL_99207.11Tetrahymena LSU hairpin poorly modeled
160HL_03785.11LSU Helix 8 (H8) Hairpin Loop
161HL_19132.11
162HL_20920.11
163HL_27397.11
164HL_37962.11

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_52574.415LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_97270.415T-loops with 1 bulged 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_24544.38LSU Helix 53 (H53) Hairpin Loop. T-loop like.
17HL_87844.38LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_11547.38LSU Helix 80 (H80) P-site Hairpin Loop.
19HL_34027.385S Loop C - Upper part of Hairpin Loop.
20HL_70420.37LSU Helix 97 Hairpin loop
21HL_87136.37LSU Helix 39A Hairpin loop
22HL_01926.47LSU Helix 71 (H71) Hairpin Loop.
23HL_39942.37LSU Helix 91 (H91) Hairpin Loop
24HL_41833.37LSU Helix 81 (H81) Hairpin Loop
25HL_34108.37LSU Helix 37 (H37) Hairpin Loop.
26HL_46489.37LSU H89 Hairpin Loop
27HL_18156.37LSU Helix 72 (H72) Hairpin Loop
28HL_39872.37LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
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_21545.23LSU Helix 96 (H96) Hairpin Loop
39HL_27429.43
40HL_64371.33SSU Central Pseudoknot (forms helix 2)
41HL_91693.23
42HL_35619.33
43HL_48254.23LSU Helix 84 (H84) Hairpin Loop.
44HL_68697.33
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_76036.33LSU Helix 8 (H8) Hairpin Loop
4HL_90579.33LSU Helix 69 (H69) Hairpin Loop
5HL_74686.13SSU Central Pseudoknot (forms helix 2)
6HL_32644.22LSU Helix 69 (H69) Hairpin Loop
7HL_84353.12
8HL_63941.12
9HL_16770.12
10HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
11HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
12HL_42969.11
13HL_30128.11
14HL_76585.11
15HL_58601.11
16HL_76679.11
17HL_33277.11
18HL_59604.11
19HL_07915.11
20HL_34440.11
21HL_35200.11
22HL_66467.11
23HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
24HL_36842.11
25HL_97971.11
26HL_28676.11
27HL_39486.11

Added motif groups

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