0.6 | 0.7

Changes in PDB files used for clustering

Release 0.6 has 185 PDB files, release 0.7 has 191 PDB files, 180 of them are identical.

1 equivalence classes changed representatives: 3UXR → 3V2F.

10 new structures in release 0.7: 3SYW, 3SZX, 3TZR, 3U4M, 3V7E, 4AOB, 4E48, 4E5C, 4ERD, 4EYA.

Obsolete: 3UXR → 4V8A.

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 0.6 has 260 motif groups, release 0.7 has 263 motif groups, 142 of them are identical.

59 motif groups were updated, 59 groups are present only in release 0.6, 62 groups are only in release 0.7.

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	IL_01239.1	5
2	IL_82188.1	5	LSU H68 IL from H.m.
3	IL_92484.1	5
4	IL_28572.1	4	16S h18 kink-turn like motif
5	IL_22732.1	4	tSH-inserted-tHS
6	IL_31066.2	4	SSU Helix 44 (h44) extension
7	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
8	IL_34363.1	3	Kink-turn from 23S H42
9	IL_37053.1	3	Kink-turn from 23S H58
10	IL_79955.2	3	SSU Helix (23) h23 IL1
11	IL_82563.1	3	Thi-box riboswitch T-loop
12	IL_15840.1	3
13	IL_52173.1	3
14	IL_30840.1	3
15	IL_62499.2	3
16	IL_98421.1	3
17	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
18	IL_95150.2	3
19	IL_12211.1	2
20	IL_81441.1	2
21	IL_25174.1	2
22	IL_46435.1	2
23	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
24	IL_28942.1	2
25	IL_40892.1	2
26	IL_70280.1	2	Double sheared with wobble cWW.
27	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
28	IL_37197.1	2
29	IL_50521.1	2
30	IL_87173.1	2
31	IL_97833.1	2
32	IL_80093.1	2
33	IL_92459.1	2
34	IL_16166.1	2
35	IL_23414.1	2
36	IL_74876.1	2
37	IL_09882.1	2
38	IL_16330.1	2
39	IL_55287.1	2
40	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
41	IL_98566.1	2
42	IL_45794.1	2
43	IL_52940.1	2
44	IL_90057.1	2
45	IL_05462.1	1
46	IL_20775.1	1	tSH-inserted
47	IL_25082.1	1
48	IL_26971.1	1
49	IL_32080.1	1
50	IL_40527.1	1	Kink-turn
51	IL_46306.1	1
52	IL_52958.1	1
53	IL_55934.1	1	kink-turn-like
54	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
55	IL_76486.1	1	Sarcin-ricin motif with syn G
56	IL_85805.1	1
57	IL_91078.1	1
58	IL_98924.1	1
59	IL_06306.1	1
60	IL_12233.1	1
61	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
62	IL_40845.1	1
63	IL_53323.1	1
64	IL_59529.1	1
65	IL_67735.1	1
66	IL_82113.1	1
67	IL_86059.1	1
68	IL_91089.1	1
69	IL_96260.1	1
70	IL_02690.1	1
71	IL_06468.1	1	16S h40 3WJ E.c.
72	IL_12486.1	1
73	IL_22579.1	1
74	IL_25181.1	1
75	IL_47687.1	1
76	IL_53988.1	1
77	IL_61723.1	1
78	IL_78809.1	1
79	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
80	IL_91904.1	1
81	IL_97073.1	1
82	IL_02835.1	1
83	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
84	IL_15205.1	1
85	IL_29949.1	1
86	IL_41009.1	1
87	IL_54450.1	1
88	IL_61730.1	1
89	IL_71685.1	1	Sarcin-like with an intercalated basepair
90	IL_92280.1	1
91	IL_02957.1	1
92	IL_07375.1	1
93	IL_22858.1	1
94	IL_25307.1	1
95	IL_30390.1	1
96	IL_37347.1	1
97	IL_41139.1	1
98	IL_54576.1	1
99	IL_62352.1	1
100	IL_71942.1	1
101	IL_82650.1	1
102	IL_88367.1	1
103	IL_97842.1	1
104	IL_03110.1	1
105	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
106	IL_25739.1	1	M-Box Riboswitch
107	IL_37715.1	1
108	IL_41791.1	1
109	IL_52509.1	1
110	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
111	IL_80505.1	1
112	IL_83250.1	1	16S h40 3WJ T.th.
113	IL_88403.1	1
114	IL_03741.1	1
115	IL_23639.1	1	tWH-tHS-L-cWW
116	IL_26241.1	1
117	IL_37990.1	1
118	IL_43316.1	1
119	IL_52752.1	1
120	IL_63952.1	1
121	IL_75415.1	1	Pseudo-knot forming internal loop
122	IL_80652.1	1
123	IL_83920.1	1
124	IL_05221.1	1
125	IL_11302.1	1
126	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
127	IL_24143.1	1	Yeast 18S
128	IL_26868.1	1
129	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
130	IL_39324.1	1
131	IL_55649.1	1
132	IL_65788.1	1
133	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
134	IL_81398.1	1
135	IL_85510.1	1
136	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.2	234
2	IL_47174.2	200	16S h34 ILa : Part of larger motif
3	IL_39199.2	55	Hoogsteen-edge Platform, Single bulged base
4	IL_41766.2	49	Tandem cWW pairs (Not AU or GC)
5	IL_56465.2	45	Single, unpaired intercalated base, consensus A
6	IL_44540.2	43	Sugar-edge, 1-base platform, consensus tHS
7	IL_87904.2	31	Triple sheared
8	IL_13959.2	24	Double Sheared (tSH-tHS)
9	IL_93424.2	22	tSH-inserted-tHW
10	IL_32390.2	21	16S h19 IL and 23S H41 IL
11	IL_65553.2	21	Kink-turn
12	IL_55938.2	19	LSU Helix 89 (H89) IL2. cSH Platform.
13	IL_92027.2	17	16S h21 S8 binding site
14	IL_85647.2	16	Sarcin-ricin parent motif with 15 Nts
15	IL_31555.2	15	16S decoding site
16	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17	IL_94430.2	14	16S h32-h33-h34 3WJ
18	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19	IL_40090.2	11	16S h34 ILa : Part of larger motif
20	IL_27618.2	11	23S H73 ILa : Part of larger Motif
21	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
22	IL_58291.2	9	Recurrent Sub-motif found in junctions
23	IL_47444.2	9	SRP Loop E-like motif
24	IL_92114.2	9	GAAA loop receptor "platform" motif
25	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26	IL_90459.2	8	cWW AG or UU
27	IL_86357.2	7	LSU Helix 61 IL2
28	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
29	IL_73000.2	7	cHS-cWS
30	IL_97057.2	6
31	IL_70237.3	6
32	IL_53635.2	6	LSU Helix 32 (H32) IL
33	IL_72158.2	6	LSU Helix 62 (H62) IL
34	IL_13069.2	6	LSU 3WJ H32-H33-H35A
35	IL_24022.2	6
36	IL_25230.2	6	Bacterial 5S rRNA Loop E
37	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
38	IL_45262.2	5
39	IL_79083.2	5
40	IL_78732.3	5	Double S-turn motif
41	IL_80179.2	5
42	IL_40387.2	5
43	IL_02359.2	5
44	IL_64184.2	4
45	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
46	IL_98591.2	4
47	IL_39526.2	4
48	IL_38807.2	4
49	IL_09348.2	3
50	IL_16252.2	3	23S H91 IL
51	IL_34628.2	3	Kink-turn
52	IL_58586.2	3
53	IL_34156.2	3	cWW AG or UU
54	IL_23262.3	3
55	IL_80494.2	3	LSU H58 IL2 H.m.
56	IL_76095.3	2	Motif from Hairpin Ribozyme
57	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
58	IL_82831.2	2	Kink-turn from 16S H23
59	IL_41397.2	2	LSU Helix 96 (H96) IL2

Removed motif groups

#	Motif id	Instances	Description
1	IL_11616.1	55	cWH basepair with syn base
2	IL_54307.1	27	C-loop
3	IL_73663.1	15	1 or 2 bulged bases
4	IL_48187.1	11	Single sheared with bulged bases
5	IL_99515.1	11	23S H91 IL
6	IL_68939.1	9	Kink-turn from U4
7	IL_76831.1	8	REV element IL with syn G
8	IL_40239.1	8	Leadzyme Motif
9	IL_82367.4	7
10	IL_29610.1	6
11	IL_24476.1	5
12	IL_78157.1	5
13	IL_92936.1	5
14	IL_93335.2	5
15	IL_59016.1	5
16	IL_18947.1	4
17	IL_69124.1	4
18	IL_11167.3	4
19	IL_49111.1	4	tHS tHH bulge with S-turn
20	IL_11594.1	4
21	IL_92333.1	4
22	IL_30979.1	3
23	IL_10804.1	3
24	IL_13740.1	3
25	IL_99434.1	3	Single-Base Intercalation Site
26	IL_62718.1	2
27	IL_19202.1	2
28	IL_63741.1	2
29	IL_91543.1	2
30	IL_19889.1	2
31	IL_75449.1	2
32	IL_92123.1	2
33	IL_67117.1	2
34	IL_68736.1	2
35	IL_02691.1	2
36	IL_44742.1	2
37	IL_57870.1	2
38	IL_88684.1	2
39	IL_09390.1	2
40	IL_47247.1	2
41	IL_69009.1	2
42	IL_89461.1	2
43	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
44	IL_91513.1	1
45	IL_31793.1	1	Kink-turn from 16S H23
46	IL_48650.1	1
47	IL_38333.1	1
48	IL_65978.1	1
49	IL_24335.1	1
50	IL_39165.1	1
51	IL_50767.1	1
52	IL_39230.1	1
53	IL_67697.1	1
54	IL_55167.1	1
55	IL_14225.1	1
56	IL_29877.1	1
57	IL_99165.1	1
58	IL_17109.1	1
59	IL_30650.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_06390.1	25	cWH basepair with syn base
2	IL_73276.1	20	C-loop
3	IL_06429.1	16	16S h19 IL and 23S H41 IL \| 1 or 2 bulged bases
4	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
6	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
7	IL_89088.1	6	16S h19 IL and 23S H41 IL
8	IL_08926.1	6	23S H91 IL
9	IL_10007.1	6	Single sheared with bulged bases
10	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
11	IL_07911.1	5
12	IL_77263.1	5	Kink-turn from U4
13	IL_21333.1	4	tSH-tHW-bulge
14	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
15	IL_98556.1	4
16	IL_53774.1	3	Single sheared with bulged bases
17	IL_71565.1	3
18	IL_43946.1	3
19	IL_45808.1	3
20	IL_75447.1	3
21	IL_12068.1	2
22	IL_87548.1	2
23	IL_99575.1	2
24	IL_12269.1	2
25	IL_43933.1	2
26	IL_74291.1	2
27	IL_21495.1	2
28	IL_91026.1	2
29	IL_14023.1	2
30	IL_00998.1	2
31	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
32	IL_31707.1	2	Vitamin B12 aptamer
33	IL_78674.1	2	tHS tHH bulge with S-turn
34	IL_01054.1	2
35	IL_37406.1	2
36	IL_48285.1	2	Leadzyme Motif
37	IL_65137.1	2	Kink-turn like motif in Group I Intron
38	IL_18755.1	1
39	IL_41849.1	1
40	IL_53423.1	1
41	IL_12507.1	1
42	IL_56513.1	1
43	IL_89794.1	1
44	IL_07675.1	1	tHS tHH bulge with S-turn
45	IL_13682.1	1
46	IL_21421.1	1
47	IL_56779.1	1
48	IL_90880.1	1
49	IL_13942.1	1
50	IL_57977.1	1
51	IL_31241.1	1
52	IL_47457.1	1
53	IL_58454.1	1
54	IL_95939.1	1
55	IL_60643.1	1
56	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
57	IL_11869.1	1
58	IL_17603.1	1
59	IL_82601.1	1	Tandem cWW water-inserted CU pairs