1.13 | 1.14

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: 3V2F → 4NVV.

4 new structures in release 1.14: 1VW3, 1VW4, 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_57514.2	6	Two base, cross-stacked hairpin loop
8	HL_06643.3	6	tRNA D-loop. Sec tRNA
9	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
10	HL_72273.1	5	tRNA D-loop
11	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
12	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
13	HL_45018.3	5	Hairpin-Hairpin Interacting HL
14	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
15	HL_86115.1	4
16	HL_25124.2	4	tSW GA closed tetraloops
17	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
18	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
19	HL_62881.1	4	RNase P Structured Hairpin Loop
20	HL_98523.2	4	GNRA-like. Closed by tSH UC.
21	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
22	HL_80492.2	3	tRNA D-loop
23	HL_98833.3	3
24	HL_76766.4	3
25	HL_19221.2	3
26	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
27	HL_23182.1	3
28	HL_78361.1	3
29	HL_58083.2	3
30	HL_06997.2	3
31	HL_41827.1	3
32	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
33	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
34	HL_18587.1	2
35	HL_90542.1	2
36	HL_24711.1	2
37	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
38	HL_91872.1	2
39	HL_23129.1	2
40	HL_38130.2	2
41	HL_42553.1	2
42	HL_60200.1	2
43	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
44	HL_96915.1	2
45	HL_99633.1	2
46	HL_05361.1	2
47	HL_86398.1	2
48	HL_06122.1	2
49	HL_19399.1	2
50	HL_49210.1	2
51	HL_54751.2	2
52	HL_65249.1	2
53	HL_23290.1	2
54	HL_33451.1	2
55	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
56	HL_87554.1	2
57	HL_93771.1	2	tRNA T-loop distorted by RS binding
58	HL_19528.1	2
59	HL_26495.1	2
60	HL_74505.1	2
61	HL_94578.1	2
62	HL_17790.1	2	UNCG-like. cWW Closing pair.
63	HL_24473.3	2	tRNA D-loop
64	HL_42094.1	2
65	HL_50312.1	2
66	HL_62967.1	2
67	HL_65924.1	2
68	HL_74559.1	2	Two base, cross-stacked hairpin loop
69	HL_98577.1	2
70	HL_01418.1	1
71	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
72	HL_20806.1	1
73	HL_24707.1	1
74	HL_35865.1	1
75	HL_42345.1	1
76	HL_46570.1	1
77	HL_52116.1	1
78	HL_56775.1	1
79	HL_59225.1	1
80	HL_62970.1	1
81	HL_70912.1	1
82	HL_75850.1	1
83	HL_85018.1	1
84	HL_95716.1	1
85	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
86	HL_19132.1	1
87	HL_20920.1	1
88	HL_27397.1	1
89	HL_37962.1	1
90	HL_47337.1	1
91	HL_52540.1	1
92	HL_56809.1	1
93	HL_59610.1	1
94	HL_63304.1	1
95	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
96	HL_82243.1	1
97	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
98	HL_04194.1	1
99	HL_12706.1	1
100	HL_29196.1	1
101	HL_53015.1	1
102	HL_57217.1	1	cHS platform Intercalation Site
103	HL_67000.1	1
104	HL_77692.1	1	tRNA D-loop
105	HL_82288.1	1
106	HL_93263.1	1
107	HL_19226.1	1
108	HL_25175.1	1
109	HL_30008.1	1
110	HL_38138.1	1
111	HL_48480.1	1
112	HL_53789.1	1
113	HL_60203.1	1
114	HL_65071.1	1
115	HL_67761.1	1
116	HL_73465.1	1
117	HL_78228.1	1
118	HL_93530.1	1
119	HL_96994.1	1
120	HL_13786.1	1
121	HL_23195.1	1
122	HL_25195.1	1
123	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
124	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
125	HL_44390.1	1
126	HL_57843.1	1
127	HL_68435.1	1
128	HL_73972.1	1
129	HL_83865.1	1
130	HL_87223.1	1
131	HL_93567.1	1
132	HL_97499.1	1
133	HL_19452.1	1	tRNA D-loop
134	HL_25197.1	1
135	HL_39422.1	1
136	HL_44522.1	1
137	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
138	HL_55202.1	1	U2B"-U2A" binding hairpin loop
139	HL_62880.1	1
140	HL_68579.1	1
141	HL_78420.1	1
142	HL_84289.1	1
143	HL_97784.1	1
144	HL_17537.1	1
145	HL_24108.1	1
146	HL_33640.1	1
147	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
148	HL_55272.1	1
149	HL_58223.1	1
150	HL_65802.1	1
151	HL_68733.1	1	LSU Yeast Hairpin Loop
152	HL_78507.1	1
153	HL_84768.1	1
154	HL_88960.1	1
155	HL_00090.1	1
156	HL_10116.1	1	Kink-turn-like Hairpin Loop
157	HL_26579.1	1
158	HL_45411.1	1
159	HL_59182.1	1
160	HL_69403.1	1	GNRA-like
161	HL_79902.1	1
162	HL_84888.1	1	T-loop like but without tWH UA
163	HL_90102.1	1	Kink-turn-like Hairpin Loop
164	HL_95049.1	1	Two base, cross-stacked hairpin loop

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_97270.4	15	T-loops with 1 bulged base
7	HL_52574.4	15	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked 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_11547.3	8	LSU Helix 80 (H80) P-site Hairpin Loop.
17	HL_34027.3	8	5S Loop C - Upper part of Hairpin Loop.
18	HL_24544.3	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19	HL_87844.3	8	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
20	HL_41833.3	7	LSU Helix 81 (H81) Hairpin Loop
21	HL_34108.3	7	LSU Helix 37 (H37) Hairpin Loop.
22	HL_46489.3	7	LSU H89 Hairpin Loop
23	HL_18156.3	7	LSU Helix 72 (H72) Hairpin Loop
24	HL_39872.3	7	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25	HL_70420.3	7	LSU Helix 97 Hairpin loop
26	HL_87136.3	7	LSU Helix 39A Hairpin loop
27	HL_01926.4	7	LSU Helix 71 (H71) Hairpin Loop.
28	HL_39942.3	7	LSU Helix 91 (H91) Hairpin Loop
29	HL_75579.3	6
30	HL_88311.3	6	LSU Helix 35 (H35) Hairpin Loop
31	HL_11509.3	6	LSU Helix 6 (H6) Hairpin Loop.
32	HL_62228.4	6	LSU Helix 35A (H35A) Hairpin Loop
33	HL_85534.2	6	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
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_27429.4	3
39	HL_64371.3	3	SSU Central Pseudoknot (forms helix 2)
40	HL_91693.2	3
41	HL_35619.3	3
42	HL_48254.2	3	LSU Helix 84 (H84) Hairpin Loop.
43	HL_68697.3	3
44	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
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_16770.1	2
7	HL_21675.3	2	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
9	HL_32644.2	2	LSU Helix 69 (H69) Hairpin Loop
10	HL_84353.1	2
11	HL_63941.1	2
12	HL_35200.1	1
13	HL_66467.1	1
14	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
15	HL_36842.1	1
16	HL_97971.1	1
17	HL_28676.1	1
18	HL_39486.1	1
19	HL_42969.1	1
20	HL_30128.1	1
21	HL_76585.1	1
22	HL_58601.1	1
23	HL_76679.1	1
24	HL_33277.1	1
25	HL_59604.1	1
26	HL_07915.1	1
27	HL_34440.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_89236.1	6	LSU Helix 69 (H69) Hairpin Loop
2	HL_86077.1	5	GNRA with one bulged base \| GNRA-like with bulged base.
3	HL_31318.1	5	SSU Central Pseudoknot (forms helix 2)
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_10075.1	1
21	HL_46055.1	1
22	HL_63997.1	1
23	HL_99612.1	1
24	HL_10894.1	1
25	HL_49998.1	1
26	HL_99932.1	1
27	HL_50018.1	1
28	HL_19363.1	1
29	HL_93428.1	1
30	HL_27236.1	1
31	HL_53116.1	1
32	HL_82622.1	1	SSU Central Pseudoknot (forms helix 2)
33	HL_04305.1	1
34	HL_59982.1	1
35	HL_85982.1	1
36	HL_97022.1	1