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_82538.57LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7HL_42677.27
8HL_06643.36tRNA D-loop. Sec tRNA
9HL_20199.16SSU Central Pseudoknot (forms helix 2) | LSU Helix 69 (H69) Hairpin Loop | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
10HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
11HL_64543.46SSU Helix 31 (h31) Hairpin Loop
12HL_08382.45
13HL_72273.15tRNA D-loop
14HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
15HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
16HL_82418.24LSU Helix 8 (H8) Hairpin Loop
17HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
18HL_25124.24tSW GA closed tetraloops
19HL_18587.34
20HL_66677.24
21HL_62881.14RNase P Structured Hairpin Loop
22HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
23HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
24HL_11376.14LSU Helix 8 (H8) Hairpin Loop
25HL_72846.14LSU Helix 69 (H69) Hairpin Loop
26HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
27HL_42094.23
28HL_58083.33
29HL_74307.13
30HL_84911.13
31HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
32HL_27429.53
33HL_28339.23
34HL_76766.43
35HL_91693.23
36HL_59516.13cHS GU/cWS Double Platform creates Intercalation site
37HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
38HL_98833.33
39HL_19221.23
40HL_21419.23UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
41HL_41827.13
42HL_60200.23
43HL_80492.23tRNA D-loop
44HL_06122.23
45HL_21545.23LSU Helix 96 (H96) Hairpin Loop
46HL_55684.13
47HL_65249.23
48HL_78361.13
49HL_01389.12
50HL_24711.12
51HL_33451.12
52HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
53HL_49210.12
54HL_65924.12
55HL_70383.12GNRA-like
56HL_93771.12tRNA T-loop distorted by RS binding
57HL_20004.12
58HL_27478.12
59HL_34912.12
60HL_35652.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
61HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
62HL_54719.12Two base, cross-stacked hairpin loop
63HL_57263.12
64HL_84172.12
65HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
66HL_98577.12
67HL_26495.12
68HL_42553.12
69HL_46388.12
70HL_50312.12
71HL_77391.12
72HL_41700.12
73HL_50937.12
74HL_64438.12Kink-turn-like Hairpin Loop
75HL_87554.12
76HL_05361.12
77HL_15793.12UNCG-like. cWW Closing pair.
78HL_24473.32tRNA D-loop
79HL_51271.12
80HL_19399.12
81HL_38130.22
82HL_42077.32LSU Helix 28 (H28) Hairpin Loop
83HL_44467.12
84HL_13786.11
85HL_17537.11
86HL_19452.11tRNA D-loop
87HL_21695.11UNCG-like. cWW Closing pair.
88HL_27397.11
89HL_38138.11
90HL_45358.11Double hairpin loop based on GGA triple
91HL_48480.11
92HL_52540.11
93HL_56775.11
94HL_65802.11
95HL_68579.11
96HL_78389.11
97HL_93567.11
98HL_97022.11
99HL_99612.11
100HL_08203.11
101HL_14384.11
102HL_21839.11
103HL_33640.11
104HL_38898.11
105HL_42255.11
106HL_45411.11
107HL_53015.11
108HL_56809.11
109HL_58223.11
110HL_62374.11
111HL_74451.11
112HL_78422.11SSU Central Pseudoknot (forms helix 2)
113HL_85018.11
114HL_97784.11
115HL_99779.11
116HL_03785.11LSU Helix 8 (H8) Hairpin Loop
117HL_14524.11
118HL_22461.11
119HL_25175.11
120HL_39422.11
121HL_42345.11
122HL_45740.11
123HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
124HL_53789.11
125HL_57217.11cHS platform Intercalation Site
126HL_59182.11
127HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
128HL_70912.11
129HL_75624.11
130HL_78507.11
131HL_83865.11
132HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
133HL_91613.11
134HL_95049.11Two base, cross-stacked hairpin loop
135HL_98233.11
136HL_99932.11
137HL_04305.11
138HL_10075.11
139HL_14536.11
140HL_19074.11
141HL_20028.11
142HL_22533.11
143HL_25195.11
144HL_39846.11
145HL_46055.11
146HL_50018.11
147HL_59225.11
148HL_66877.11cSH GU/cWS double platform, intercalation site
149HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
150HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
151HL_10116.11Kink-turn-like Hairpin Loop
152HL_15291.11GNRA with one bulged base
153HL_19132.11
154HL_23080.11
155HL_28776.11
156HL_35865.11
157HL_55202.11U2B"-U2A" binding hairpin loop
158HL_57339.11
159HL_63997.11
160HL_66880.11
161HL_72389.11
162HL_79902.11
163HL_84289.11
164HL_87223.11
165HL_05113.11
166HL_11257.11
167HL_20806.11
168HL_24108.11
169HL_26579.11
170HL_30008.11
171HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
172HL_46570.11
173HL_55272.11
174HL_57644.11
175HL_59610.11
176HL_67000.11
177HL_77692.11tRNA D-loop
178HL_84720.11
179HL_93263.11
180HL_96012.11
181HL_98834.11
182HL_19363.11
183HL_27236.11
184HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
185HL_37962.11
186HL_44390.11
187HL_47337.11
188HL_55450.11
189HL_57667.11
190HL_67761.11
191HL_78228.11
192HL_84768.11
193HL_88960.11
194HL_93428.11
195HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
196HL_99207.11Tetrahymena LSU hairpin poorly modeled
197HL_00721.11
198HL_12706.11
199HL_17008.11Nova-2 KH3 domain binding hairpin
200HL_24707.11
201HL_30731.11
202HL_52116.11
203HL_57923.11
204HL_60203.11
205HL_68435.11
206HL_73972.11
207HL_82288.11
208HL_84888.11T-loop like but without tWH UA
209HL_89473.11
210HL_93530.11
211HL_96994.11
212HL_99584.11

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_80459.811
17HL_01926.811LSU Helix 71 (H71) Hairpin Loop.
18HL_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.
19HL_24544.611LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_34027.7115S Loop C - Upper part of Hairpin Loop.
21HL_34108.710LSU Helix 37 (H37) Hairpin Loop.
22HL_70420.710LSU Helix 97 Hairpin loop
23HL_41833.710LSU Helix 81 (H81) Hairpin Loop
24HL_87136.710LSU Helix 39A Hairpin loop
25HL_18156.710LSU Helix 72 (H72) Hairpin Loop
26HL_75579.710
27HL_46489.710LSU H89 Hairpin Loop
28HL_85534.69LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29HL_11509.78LSU Helix 6 (H6) Hairpin Loop.
30HL_57087.28Two base, cross-stacked hairpin loop
31HL_88311.78LSU Helix 35 (H35) Hairpin Loop
32HL_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
33HL_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.
34HL_99908.57LSU Helix 69 (H69) Hairpin Loop
35HL_45018.57Hairpin-Hairpin Interacting HL
36HL_62228.77LSU Helix 35A (H35A) Hairpin Loop
37HL_00311.27SSU Central Pseudoknot (forms helix 2)
38HL_66174.47cHS GU/cWS Double Platform creates Intercalation site
39HL_48254.56LSU Helix 84 (H84) Hairpin Loop.
40HL_12908.26LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_94364.25
42HL_39203.25
43HL_96915.45
44HL_86077.45GNRA with one bulged base | GNRA-like with bulged base.
45HL_43357.35SSU Central Pseudoknot (forms helix 2)
46HL_86115.35
47HL_19033.24SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
48HL_13707.34cSH AA Platform containing Hairpin Loop
49HL_31147.24SSU Central Pseudoknot (forms helix 2)
50HL_89131.24
51HL_01788.33LSU Yeast Hairpin Loop
52HL_23290.23
53HL_94578.32
54HL_64371.52SSU Central Pseudoknot (forms helix 2)

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_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
4HL_72372.15
5HL_00415.15GNRA-like. Closed by tSH UC.
6HL_34954.14
7HL_23182.24
8HL_28422.24
9HL_06997.23
10HL_15701.13
11HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
12HL_92260.12
13HL_94212.1216S helix 23 and 24 hairpin loops
14HL_69907.12
15HL_82382.12
16HL_72489.12
17HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_29892.12
19HL_49961.12
20HL_74026.12
21HL_04584.11
22HL_19673.11
23HL_50078.11
24HL_63323.11
25HL_75984.11
26HL_05350.11
27HL_50954.11
28HL_63642.11
29HL_76004.11
30HL_23628.11
31HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
32HL_65107.11
33HL_79541.1116S helix 23 and 24 hairpin loops
34HL_92594.11
35HL_08388.11
36HL_24422.11
37HL_39035.11
38HL_58052.11
39HL_65428.11
40HL_81994.11
41HL_11337.11
42HL_25197.11
43HL_39943.11
44HL_61871.11
45HL_94639.11
46HL_25947.11
47HL_40070.11
48HL_62500.11
49HL_83263.11
50HL_94813.11
51HL_16822.11
52HL_40731.11
53HL_62880.11
54HL_94981.11
55HL_63001.11
56HL_87172.11
57HL_95822.11

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_01475.14
5HL_57963.14GNRA-like. Closed by tSH UC.
6HL_13352.14
7HL_90792.14
8HL_19066.14SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
9HL_85551.14
10HL_57225.13
11HL_82098.1316S helix 23 and 24 hairpin loops
12HL_72388.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
13HL_96309.12S8 operon binding Hairpin Loop. T-loop like with purine stacking.
14HL_22952.12
15HL_43821.12
16HL_57621.12
17HL_23337.12
18HL_45343.12
19HL_05894.12
20HL_08494.12LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_52338.12
22HL_53279.12
23HL_84575.12
24HL_91125.12
25HL_00394.12
26HL_19755.11
27HL_42161.11
28HL_85802.11
29HL_03007.11
30HL_87958.11
31HL_04735.11
32HL_81815.11
33HL_88259.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
34HL_31261.11
35HL_45777.11
36HL_61400.11
37HL_89958.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
38HL_33822.11
39HL_49013.11
40HL_64778.11
41HL_83609.11
42HL_36554.11
43HL_64859.11
44HL_84030.11
45HL_16959.11
46HL_38777.11
47HL_70061.11
48HL_40222.11
49HL_56596.11
50HL_91581.11