1.13 | 1.14

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: 3V2F → 4NVV.

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

Obsolete: 3V2F → 4V8I.

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 id	Instances	Description
1	HL_74465.5	13	tRNA Anti-Codon loop
2	HL_27271.2	12	LSU Helix 96 (H96) Hairpin Loop
3	HL_48039.2	11	MS2 virus RNA Hairpin
4	HL_15603.2	9	U1A protein-binding Hairpin Loop.
5	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
6	HL_42677.2	7
7	HL_06643.3	6	tRNA D-loop. Sec tRNA
8	HL_57514.2	6	Two base, cross-stacked hairpin loop
9	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
10	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
11	HL_72273.1	5	tRNA D-loop
12	HL_45018.3	5	Hairpin-Hairpin Interacting HL
13	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
14	HL_86115.1	4
15	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
16	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
17	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
18	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
19	HL_62881.1	4	RNase P Structured Hairpin Loop
20	HL_98523.2	4	GNRA-like. Closed by tSH UC.
21	HL_25124.2	4	tSW GA closed tetraloops
22	HL_19221.2	3
23	HL_98833.3	3
24	HL_23182.1	3
25	HL_78361.1	3
26	HL_41827.1	3
27	HL_80492.2	3	tRNA D-loop
28	HL_76766.4	3
29	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
30	HL_58083.2	3
31	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
32	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
33	HL_06997.2	3
34	HL_54751.2	2
35	HL_49210.1	2
36	HL_93771.1	2	tRNA T-loop distorted by RS binding
37	HL_23290.1	2
38	HL_26495.1	2
39	HL_42553.1	2
40	HL_90542.1	2
41	HL_06122.1	2
42	HL_24473.3	2	tRNA D-loop
43	HL_33451.1	2
44	HL_87554.1	2
45	HL_86398.1	2
46	HL_74505.1	2
47	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
48	HL_17790.1	2	UNCG-like. cWW Closing pair.
49	HL_50312.1	2
50	HL_23129.1	2
51	HL_91872.1	2
52	HL_60200.1	2
53	HL_38130.2	2
54	HL_94578.1	2
55	HL_19528.1	2
56	HL_74559.1	2	Two base, cross-stacked hairpin loop
57	HL_65924.1	2
58	HL_24711.1	2
59	HL_65249.1	2
60	HL_19399.1	2
61	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
62	HL_62967.1	2
63	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
64	HL_98577.1	2
65	HL_44467.1	2
66	HL_18587.1	2
67	HL_42094.1	2
68	HL_05361.1	2
69	HL_99633.1	2
70	HL_96915.1	2
71	HL_53789.1	1
72	HL_25195.1	1
73	HL_97499.1	1
74	HL_00721.1	1
75	HL_26579.1	1
76	HL_84289.1	1
77	HL_27397.1	1
78	HL_12706.1	1
79	HL_67761.1	1
80	HL_63304.1	1
81	HL_47337.1	1
82	HL_68733.1	1	LSU Yeast Hairpin Loop
83	HL_97784.1	1
84	HL_85018.1	1
85	HL_99584.1	1
86	HL_29196.1	1
87	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
88	HL_37962.1	1
89	HL_65071.1	1
90	HL_44522.1	1
91	HL_30731.1	1
92	HL_70912.1	1
93	HL_13786.1	1
94	HL_55272.1	1
95	HL_78420.1	1
96	HL_90102.1	1	Kink-turn-like Hairpin Loop
97	HL_19452.1	1	tRNA D-loop
98	HL_08203.1	1
99	HL_20920.1	1
100	HL_84768.1	1
101	HL_77692.1	1	tRNA D-loop
102	HL_65802.1	1
103	HL_24707.1	1
104	HL_57217.1	1	cHS platform Intercalation Site
105	HL_39422.1	1
106	HL_79902.1	1
107	HL_68579.1	1
108	HL_53015.1	1
109	HL_25175.1	1
110	HL_95716.1	1
111	HL_10116.1	1	Kink-turn-like Hairpin Loop
112	HL_98233.1	1
113	HL_30008.1	1
114	HL_38138.1	1
115	HL_25197.1	1
116	HL_48480.1	1
117	HL_99779.1	1
118	HL_52540.1	1
119	HL_57843.1	1
120	HL_91613.1	1
121	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
122	HL_93530.1	1
123	HL_46570.1	1
124	HL_73465.1	1
125	HL_42345.1	1
126	HL_56775.1	1
127	HL_52116.1	1
128	HL_19226.1	1
129	HL_95049.1	1	Two base, cross-stacked hairpin loop
130	HL_05113.1	1
131	HL_19132.1	1
132	HL_67000.1	1
133	HL_62970.1	1
134	HL_04194.1	1
135	HL_82243.1	1
136	HL_83865.1	1
137	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
138	HL_96994.1	1
139	HL_55202.1	1	U2B"-U2A" binding hairpin loop
140	HL_73972.1	1
141	HL_93567.1	1
142	HL_57923.1	1
143	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
144	HL_45358.1	1	Double hairpin loop based on GGA triple
145	HL_84888.1	1	T-loop like but without tWH UA
146	HL_88960.1	1
147	HL_93263.1	1
148	HL_62880.1	1
149	HL_78228.1	1
150	HL_69403.1	1	GNRA-like
151	HL_23195.1	1
152	HL_01418.1	1
153	HL_24108.1	1
154	HL_38898.1	1
155	HL_59610.1	1
156	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
157	HL_35865.1	1
158	HL_45411.1	1
159	HL_20806.1	1
160	HL_60203.1	1
161	HL_68435.1	1
162	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
163	HL_44390.1	1
164	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
165	HL_75850.1	1
166	HL_82288.1	1
167	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
168	HL_20028.1	1
169	HL_59182.1	1
170	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
171	HL_33640.1	1
172	HL_78507.1	1
173	HL_87223.1	1
174	HL_58223.1	1
175	HL_66880.1	1
176	HL_56809.1	1
177	HL_00090.1	1
178	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
179	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
180	HL_17537.1	1
181	HL_59225.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.13	238	GNRA Hairpin motifs
2	HL_72498.13	67	T-loops with two bulged bases
3	HL_39895.7	35	UNCG Hairpin motifs
4	HL_18781.5	21	Double sheared (tSH) with U-turn
5	HL_91226.4	17	Kissing Hairpin motif
6	HL_52574.4	15	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7	HL_97270.4	15	T-loops with 1 bulged base
8	HL_49036.4	12	LSU Helix 11 (H11) Hairpin Loop. GNRA-like. \| GNRA with one bulged base
9	HL_56824.3	11	LSU Helix 60A. LSU Helix 63A.
10	HL_46175.3	11	16S helix 23 and 24 hairpin loops
11	HL_75759.5	10
12	HL_17723.5	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13	HL_68081.4	10	LSU Helix 20 Hairpin loop
14	HL_33402.4	9	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
15	HL_80459.4	9
16	HL_24544.3	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
17	HL_87844.3	8	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18	HL_11547.3	8	LSU Helix 80 (H80) P-site Hairpin Loop.
19	HL_34027.3	8	5S Loop C - Upper part of Hairpin Loop.
20	HL_39872.3	7	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
21	HL_70420.3	7	LSU Helix 97 Hairpin loop
22	HL_87136.3	7	LSU Helix 39A Hairpin loop
23	HL_01926.4	7	LSU Helix 71 (H71) Hairpin Loop.
24	HL_39942.3	7	LSU Helix 91 (H91) Hairpin Loop
25	HL_41833.3	7	LSU Helix 81 (H81) Hairpin Loop
26	HL_34108.3	7	LSU Helix 37 (H37) Hairpin Loop.
27	HL_46489.3	7	LSU H89 Hairpin Loop
28	HL_18156.3	7	LSU Helix 72 (H72) Hairpin Loop
29	HL_85534.2	6	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
30	HL_75579.3	6
31	HL_88311.3	6	LSU Helix 35 (H35) Hairpin Loop
32	HL_11509.3	6	LSU Helix 6 (H6) Hairpin Loop.
33	HL_62228.4	6	LSU Helix 35A (H35A) Hairpin Loop
34	HL_78731.2	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
35	HL_82538.2	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
36	HL_08382.3	4
37	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
38	HL_48254.2	3	LSU Helix 84 (H84) Hairpin Loop.
39	HL_68697.3	3
40	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
41	HL_27429.4	3
42	HL_64371.3	3	SSU Central Pseudoknot (forms helix 2)
43	HL_91693.2	3
44	HL_35619.3	3
45	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop

Removed motif groups

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

Added motif groups

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