Changes in PDB files used for clustering

Release 1.17 has 263 PDB files, release 1.18 has 268 PDB files, 259 of them are identical.

2 equivalence classes changed representatives: 4TUX4TV0, 4LCK4TZZ.

7 new structures in release 1.18: 4PDB, 4QJD, 4QJH, 4R0D, 4TZX, 4W21, 4W23.

Obsolete: 1VWW4W1Z, 1VX24W28.

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 1.17 has 323 motif groups, release 1.18 has 316 motif groups, 212 of them are identical.

54 motif groups were updated, 57 groups are present only in release 1.17, 50 groups are only in release 1.18.

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_91226.723Kissing Hairpin motif
2HL_27271.415LSU Helix 96 (H96) Hairpin Loop
3HL_17723.610LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
4HL_39872.69LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
5HL_15603.29U1A protein-binding Hairpin Loop.
6HL_42677.27
7HL_82538.57LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8HL_20199.16SSU Central Pseudoknot (forms helix 2) | LSU Helix 69 (H69) Hairpin Loop | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
9HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
10HL_64543.46SSU Helix 31 (h31) Hairpin Loop
11HL_06643.36tRNA D-loop. Sec tRNA
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_08382.45
15HL_62881.14RNase P Structured Hairpin Loop
16HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
17HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
18HL_11376.14LSU Helix 8 (H8) Hairpin Loop
19HL_72846.14LSU Helix 69 (H69) Hairpin Loop
20HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
21HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
22HL_82418.24LSU Helix 8 (H8) Hairpin Loop
23HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
24HL_25124.24tSW GA closed tetraloops
25HL_18587.34
26HL_66677.24
27HL_28339.23
28HL_76766.43
29HL_91693.23
30HL_59516.13cHS GU/cWS Double Platform creates Intercalation site
31HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
32HL_98833.33
33HL_19221.23
34HL_21419.23UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
35HL_41827.13
36HL_60200.23
37HL_80492.23tRNA D-loop
38HL_06122.23
39HL_21545.23LSU Helix 96 (H96) Hairpin Loop
40HL_55684.13
41HL_65249.23
42HL_78361.13
43HL_42094.23
44HL_58083.33
45HL_74307.13
46HL_84911.13
47HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
48HL_27429.53
49HL_35652.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
50HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
51HL_54719.12Two base, cross-stacked hairpin loop
52HL_57263.12
53HL_84172.12
54HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
55HL_98577.12
56HL_26495.12
57HL_42553.12
58HL_46388.12
59HL_50312.12
60HL_77391.12
61HL_41700.12
62HL_50937.12
63HL_64438.12Kink-turn-like Hairpin Loop
64HL_87554.12
65HL_05361.12
66HL_15793.12UNCG-like. cWW Closing pair.
67HL_24473.32tRNA D-loop
68HL_51271.12
69HL_19399.12
70HL_38130.22
71HL_42077.32LSU Helix 28 (H28) Hairpin Loop
72HL_44467.12
73HL_01389.12
74HL_24711.12
75HL_33451.12
76HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
77HL_49210.12
78HL_65924.12
79HL_70383.12GNRA-like
80HL_93771.12tRNA T-loop distorted by RS binding
81HL_20004.12
82HL_27478.12
83HL_34912.12
84HL_04305.11
85HL_10075.11
86HL_14536.11
87HL_19074.11
88HL_20028.11
89HL_22533.11
90HL_25195.11
91HL_39846.11
92HL_46055.11
93HL_50018.11
94HL_59225.11
95HL_66877.11cSH GU/cWS double platform, intercalation site
96HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
97HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
98HL_10116.11Kink-turn-like Hairpin Loop
99HL_15291.11GNRA with one bulged base
100HL_19132.11
101HL_23080.11
102HL_28776.11
103HL_35865.11
104HL_55202.11U2B"-U2A" binding hairpin loop
105HL_57339.11
106HL_63997.11
107HL_66880.11
108HL_72389.11
109HL_79902.11
110HL_84289.11
111HL_87223.11
112HL_05113.11
113HL_11257.11
114HL_20806.11
115HL_24108.11
116HL_26579.11
117HL_30008.11
118HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
119HL_46570.11
120HL_55272.11
121HL_57644.11
122HL_59610.11
123HL_67000.11
124HL_77692.11tRNA D-loop
125HL_84720.11
126HL_93263.11
127HL_96012.11
128HL_98834.11
129HL_19363.11
130HL_27236.11
131HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
132HL_37962.11
133HL_44390.11
134HL_47337.11
135HL_55450.11
136HL_57667.11
137HL_67761.11
138HL_78228.11
139HL_84768.11
140HL_88960.11
141HL_93428.11
142HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
143HL_99207.11Tetrahymena LSU hairpin poorly modeled
144HL_00721.11
145HL_12706.11
146HL_17008.11Nova-2 KH3 domain binding hairpin
147HL_24707.11
148HL_30731.11
149HL_52116.11
150HL_57923.11
151HL_60203.11
152HL_68435.11
153HL_73972.11
154HL_82288.11
155HL_84888.11T-loop like but without tWH UA
156HL_89473.11
157HL_93530.11
158HL_96994.11
159HL_99584.11
160HL_13786.11
161HL_17537.11
162HL_19452.11tRNA D-loop
163HL_21695.11UNCG-like. cWW Closing pair.
164HL_27397.11
165HL_38138.11
166HL_45358.11Double hairpin loop based on GGA triple
167HL_48480.11
168HL_52540.11
169HL_56775.11
170HL_65802.11
171HL_68579.11
172HL_78389.11
173HL_93567.11
174HL_97022.11
175HL_99612.11
176HL_08203.11
177HL_14384.11
178HL_21839.11
179HL_33640.11
180HL_38898.11
181HL_42255.11
182HL_45411.11
183HL_53015.11
184HL_56809.11
185HL_58223.11
186HL_62374.11
187HL_74451.11
188HL_78422.11SSU Central Pseudoknot (forms helix 2)
189HL_85018.11
190HL_97784.11
191HL_99779.11
192HL_03785.11LSU Helix 8 (H8) Hairpin Loop
193HL_14524.11
194HL_22461.11
195HL_25175.11
196HL_39422.11
197HL_42345.11
198HL_45740.11
199HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
200HL_53789.11
201HL_57217.11cHS platform Intercalation Site
202HL_59182.11
203HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
204HL_70912.11
205HL_75624.11
206HL_78507.11
207HL_83865.11
208HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
209HL_91613.11
210HL_95049.11Two base, cross-stacked hairpin loop
211HL_98233.11
212HL_99932.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.17328GNRA Hairpin motifs
2HL_72498.1778T-loops with two bulged bases
3HL_39895.1146UNCG Hairpin motifs
4HL_18781.930Double sheared (tSH) with U-turn
5HL_97270.821T-loops with 1 bulged base
6HL_74411.318GNRA with one bulged base | GNRA-like with bulged base. | GNRA with one bulged base | GNRA Hairpin motifs | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
7HL_74465.718tRNA Anti-Codon loop
8HL_46175.617SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops
9HL_75759.916
10HL_33402.815LSU Helix 13 (H13) Hairpin loop. GNRA-like.
11HL_56824.714LSU Helix 60A. LSU Helix 63A.
12HL_68081.813LSU Helix 20 Hairpin loop
13HL_82294.613SSU Helix 37 (h37) Hairpin loop.
14HL_48039.412MS2 virus RNA Hairpin
15HL_48507.312LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
16HL_11547.711LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop. | LSU Helix 80 (H80) P-site Hairpin Loop.
17HL_24544.611LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_34027.7115S Loop C - Upper part of Hairpin Loop.
19HL_80459.811
20HL_01926.811LSU Helix 71 (H71) Hairpin Loop.
21HL_41833.710LSU Helix 81 (H81) Hairpin Loop
22HL_87136.710LSU Helix 39A Hairpin loop
23HL_18156.710LSU Helix 72 (H72) Hairpin Loop
24HL_75579.710
25HL_46489.710LSU H89 Hairpin Loop
26HL_34108.710LSU Helix 37 (H37) Hairpin Loop.
27HL_70420.710LSU Helix 97 Hairpin loop
28HL_85534.69LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29HL_57087.28Two base, cross-stacked hairpin loop
30HL_88311.78LSU Helix 35 (H35) Hairpin Loop
31HL_11509.78LSU Helix 6 (H6) Hairpin Loop.
32HL_27353.27UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
33HL_99908.57LSU Helix 69 (H69) Hairpin Loop
34HL_45018.57Hairpin-Hairpin Interacting HL
35HL_62228.77LSU Helix 35A (H35A) Hairpin Loop
36HL_00311.27SSU Central Pseudoknot (forms helix 2)
37HL_66174.47cHS GU/cWS Double Platform creates Intercalation site
38HL_19626.47LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
39HL_12908.26LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_48254.56LSU Helix 84 (H84) Hairpin Loop.
41HL_86077.45GNRA with one bulged base | GNRA-like with bulged base.
42HL_43357.35SSU Central Pseudoknot (forms helix 2)
43HL_86115.35
44HL_94364.25
45HL_39203.25
46HL_96915.45
47HL_13707.34cSH AA Platform containing Hairpin Loop
48HL_31147.24SSU Central Pseudoknot (forms helix 2)
49HL_89131.24
50HL_19033.24SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
51HL_01788.33LSU Yeast Hairpin Loop
52HL_23290.23
53HL_64371.52SSU Central Pseudoknot (forms helix 2)
54HL_94578.32

Removed motif groups

#Motif idInstancesDescription
1HL_37020.220LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
2HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
3HL_72372.15
4HL_00415.15GNRA-like. Closed by tSH UC.
5HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
6HL_28422.24
7HL_34954.14
8HL_23182.24
9HL_15701.13
10HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
11HL_06997.23
12HL_94212.1216S helix 23 and 24 hairpin loops
13HL_69907.12
14HL_82382.12
15HL_72489.12
16HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
17HL_29892.12
18HL_49961.12
19HL_74026.12
20HL_92260.12
21HL_08388.11
22HL_24422.11
23HL_39035.11
24HL_58052.11
25HL_65428.11
26HL_81994.11
27HL_11337.11
28HL_25197.11
29HL_39943.11
30HL_61871.11
31HL_94639.11
32HL_25947.11
33HL_40070.11
34HL_62500.11
35HL_83263.11
36HL_94813.11
37HL_16822.11
38HL_40731.11
39HL_62880.11
40HL_94981.11
41HL_63001.11
42HL_87172.11
43HL_95822.11
44HL_04584.11
45HL_19673.11
46HL_50078.11
47HL_63323.11
48HL_75984.11
49HL_05350.11
50HL_50954.11
51HL_63642.11
52HL_76004.11
53HL_23628.11
54HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
55HL_65107.11
56HL_79541.1116S helix 23 and 24 hairpin loops
57HL_92594.11

Added motif groups

#Motif idInstancesDescription
1HL_71179.120LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop. | LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
2HL_90506.19LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
3HL_80263.15
4HL_13352.14
5HL_90792.14
6HL_19066.14SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
7HL_85551.14
8HL_01475.14
9HL_57963.14GNRA-like. Closed by tSH UC.
10HL_82098.1316S helix 23 and 24 hairpin loops
11HL_57225.13
12HL_05894.12
13HL_08494.12LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
14HL_52338.12
15HL_53279.12
16HL_84575.12
17HL_91125.12
18HL_00394.12
19HL_72388.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
20HL_96309.12S8 operon binding Hairpin Loop. T-loop like with purine stacking.
21HL_22952.12
22HL_43821.12
23HL_57621.12
24HL_23337.12
25HL_45343.12
26HL_31261.11
27HL_45777.11
28HL_61400.11
29HL_89958.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
30HL_33822.11
31HL_49013.11
32HL_64778.11
33HL_83609.11
34HL_36554.11
35HL_64859.11
36HL_84030.11
37HL_16959.11
38HL_38777.11
39HL_70061.11
40HL_40222.11
41HL_56596.11
42HL_91581.11
43HL_19755.11
44HL_42161.11
45HL_85802.11
46HL_03007.11
47HL_87958.11
48HL_04735.11
49HL_81815.11
50HL_88259.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base