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_06643.3	6	tRNA D-loop. Sec tRNA
8	HL_57514.2	6	Two base, cross-stacked hairpin loop
9	HL_45018.3	5	Hairpin-Hairpin Interacting HL
10	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
11	HL_72273.1	5	tRNA D-loop
12	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
13	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
14	HL_62881.1	4	RNase P Structured Hairpin Loop
15	HL_98523.2	4	GNRA-like. Closed by tSH UC.
16	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
17	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
18	HL_86115.1	4
19	HL_25124.2	4	tSW GA closed tetraloops
20	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
21	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
22	HL_58083.2	3
23	HL_06997.2	3
24	HL_41827.1	3
25	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
26	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
27	HL_80492.2	3	tRNA D-loop
28	HL_98833.3	3
29	HL_76766.4	3
30	HL_19221.2	3
31	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
32	HL_23182.1	3
33	HL_78361.1	3
34	HL_23290.1	2
35	HL_33451.1	2
36	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
37	HL_87554.1	2
38	HL_93771.1	2	tRNA T-loop distorted by RS binding
39	HL_19528.1	2
40	HL_26495.1	2
41	HL_74505.1	2
42	HL_94578.1	2
43	HL_17790.1	2	UNCG-like. cWW Closing pair.
44	HL_24473.3	2	tRNA D-loop
45	HL_42094.1	2
46	HL_50312.1	2
47	HL_62967.1	2
48	HL_65924.1	2
49	HL_74559.1	2	Two base, cross-stacked hairpin loop
50	HL_98577.1	2
51	HL_18587.1	2
52	HL_90542.1	2
53	HL_24711.1	2
54	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
55	HL_91872.1	2
56	HL_23129.1	2
57	HL_38130.2	2
58	HL_42553.1	2
59	HL_60200.1	2
60	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
61	HL_96915.1	2
62	HL_99633.1	2
63	HL_05361.1	2
64	HL_86398.1	2
65	HL_06122.1	2
66	HL_19399.1	2
67	HL_49210.1	2
68	HL_54751.2	2
69	HL_65249.1	2
70	HL_19452.1	1	tRNA D-loop
71	HL_25197.1	1
72	HL_39422.1	1
73	HL_44522.1	1
74	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
75	HL_55202.1	1	U2B"-U2A" binding hairpin loop
76	HL_62880.1	1
77	HL_68579.1	1
78	HL_78420.1	1
79	HL_84289.1	1
80	HL_97784.1	1
81	HL_17537.1	1
82	HL_24108.1	1
83	HL_33640.1	1
84	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
85	HL_55272.1	1
86	HL_58223.1	1
87	HL_65802.1	1
88	HL_68733.1	1	LSU Yeast Hairpin Loop
89	HL_78507.1	1
90	HL_84768.1	1
91	HL_88960.1	1
92	HL_00090.1	1
93	HL_10116.1	1	Kink-turn-like Hairpin Loop
94	HL_26579.1	1
95	HL_45411.1	1
96	HL_59182.1	1
97	HL_69403.1	1	GNRA-like
98	HL_79902.1	1
99	HL_84888.1	1	T-loop like but without tWH UA
100	HL_90102.1	1	Kink-turn-like Hairpin Loop
101	HL_95049.1	1	Two base, cross-stacked hairpin loop
102	HL_01418.1	1
103	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
104	HL_20806.1	1
105	HL_24707.1	1
106	HL_35865.1	1
107	HL_42345.1	1
108	HL_46570.1	1
109	HL_52116.1	1
110	HL_56775.1	1
111	HL_59225.1	1
112	HL_62970.1	1
113	HL_70912.1	1
114	HL_75850.1	1
115	HL_85018.1	1
116	HL_95716.1	1
117	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
118	HL_19132.1	1
119	HL_20920.1	1
120	HL_27397.1	1
121	HL_37962.1	1
122	HL_47337.1	1
123	HL_52540.1	1
124	HL_56809.1	1
125	HL_59610.1	1
126	HL_63304.1	1
127	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
128	HL_82243.1	1
129	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
130	HL_04194.1	1
131	HL_12706.1	1
132	HL_29196.1	1
133	HL_53015.1	1
134	HL_57217.1	1	cHS platform Intercalation Site
135	HL_67000.1	1
136	HL_77692.1	1	tRNA D-loop
137	HL_82288.1	1
138	HL_93263.1	1
139	HL_19226.1	1
140	HL_25175.1	1
141	HL_30008.1	1
142	HL_38138.1	1
143	HL_48480.1	1
144	HL_53789.1	1
145	HL_60203.1	1
146	HL_65071.1	1
147	HL_67761.1	1
148	HL_73465.1	1
149	HL_78228.1	1
150	HL_93530.1	1
151	HL_96994.1	1
152	HL_13786.1	1
153	HL_23195.1	1
154	HL_25195.1	1
155	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
156	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
157	HL_44390.1	1
158	HL_57843.1	1
159	HL_68435.1	1
160	HL_73972.1	1
161	HL_83865.1	1
162	HL_87223.1	1
163	HL_93567.1	1
164	HL_97499.1	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_68081.4	10	LSU Helix 20 Hairpin loop
12	HL_75759.5	10
13	HL_17723.5	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
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_18156.3	7	LSU Helix 72 (H72) Hairpin Loop
21	HL_39872.3	7	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
22	HL_70420.3	7	LSU Helix 97 Hairpin loop
23	HL_87136.3	7	LSU Helix 39A Hairpin loop
24	HL_01926.4	7	LSU Helix 71 (H71) Hairpin Loop.
25	HL_39942.3	7	LSU Helix 91 (H91) Hairpin Loop
26	HL_41833.3	7	LSU Helix 81 (H81) Hairpin Loop
27	HL_34108.3	7	LSU Helix 37 (H37) Hairpin Loop.
28	HL_46489.3	7	LSU H89 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_82538.2	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
35	HL_78731.2	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
36	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
37	HL_08382.3	4
38	HL_35619.3	3
39	HL_48254.2	3	LSU Helix 84 (H84) Hairpin Loop.
40	HL_68697.3	3
41	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
42	HL_27429.4	3
43	HL_64371.3	3	SSU Central Pseudoknot (forms helix 2)
44	HL_91693.2	3
45	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop

Removed motif groups

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

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_82418.1	4	LSU Helix 8 (H8) Hairpin Loop
5	HL_99908.1	4	LSU Helix 69 (H69) Hairpin Loop
6	HL_84258.1	3	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7	HL_16643.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
8	HL_79956.1	3	GNRA-like with 5'-stacking of first unpaired base.
9	HL_50461.1	2
10	HL_94309.1	2	GNRA with one bulged base
11	HL_53745.1	2
12	HL_95756.1	2
13	HL_38964.1	2	LSU Helix 84 (H84) Hairpin Loop. E.coli.
14	HL_46903.1	2
15	HL_78660.1	2
16	HL_86889.1	2	SSU Central Pseudoknot (forms helix 2)
17	HL_16728.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
18	HL_81510.1	2	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
19	HL_92635.1	2
20	HL_19363.1	1
21	HL_93428.1	1
22	HL_27236.1	1
23	HL_53116.1	1
24	HL_82622.1	1	SSU Central Pseudoknot (forms helix 2)
25	HL_04305.1	1
26	HL_59982.1	1
27	HL_85982.1	1
28	HL_97022.1	1
29	HL_10075.1	1
30	HL_46055.1	1
31	HL_63997.1	1
32	HL_99612.1	1
33	HL_10894.1	1
34	HL_49998.1	1
35	HL_99932.1	1
36	HL_50018.1	1