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_92484.1	5
2	IL_01239.1	5
3	IL_82188.1	5	LSU H68 IL from H.m.
4	IL_31066.2	4	SSU Helix 44 (h44) extension
5	IL_28572.1	4	16S h18 kink-turn like motif
6	IL_22732.1	4	tSH-inserted-tHS
7	IL_30840.1	3
8	IL_62499.2	3
9	IL_98421.1	3
10	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
11	IL_95150.2	3
12	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
13	IL_34363.1	3	Kink-turn from 23S H42
14	IL_37053.1	3	Kink-turn from 23S H58
15	IL_79955.2	3	SSU Helix (23) h23 IL1
16	IL_82563.1	3	Thi-box riboswitch T-loop
17	IL_15840.1	3
18	IL_52173.1	3
19	IL_16166.1	2
20	IL_23414.1	2
21	IL_74876.1	2
22	IL_09882.1	2
23	IL_16330.1	2
24	IL_55287.1	2
25	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
26	IL_98566.1	2
27	IL_45794.1	2
28	IL_52940.1	2
29	IL_90057.1	2
30	IL_12211.1	2
31	IL_81441.1	2
32	IL_25174.1	2
33	IL_46435.1	2
34	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
35	IL_28942.1	2
36	IL_40892.1	2
37	IL_70280.1	2	Double sheared with wobble cWW.
38	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
39	IL_37197.1	2
40	IL_50521.1	2
41	IL_87173.1	2
42	IL_97833.1	2
43	IL_80093.1	2
44	IL_92459.1	2
45	IL_03110.1	1
46	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
47	IL_25739.1	1	M-Box Riboswitch
48	IL_37715.1	1
49	IL_41791.1	1
50	IL_52509.1	1
51	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
52	IL_80505.1	1
53	IL_83250.1	1	16S h40 3WJ T.th.
54	IL_88403.1	1
55	IL_03741.1	1
56	IL_23639.1	1	tWH-tHS-L-cWW
57	IL_26241.1	1
58	IL_37990.1	1
59	IL_43316.1	1
60	IL_52752.1	1
61	IL_63952.1	1
62	IL_75415.1	1	Pseudo-knot forming internal loop
63	IL_80652.1	1
64	IL_83920.1	1
65	IL_05221.1	1
66	IL_11302.1	1
67	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
68	IL_24143.1	1	Yeast 18S
69	IL_26868.1	1
70	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
71	IL_39324.1	1
72	IL_55649.1	1
73	IL_65788.1	1
74	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
75	IL_81398.1	1
76	IL_85510.1	1
77	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
78	IL_05462.1	1
79	IL_20775.1	1	tSH-inserted
80	IL_25082.1	1
81	IL_26971.1	1
82	IL_32080.1	1
83	IL_40527.1	1	Kink-turn
84	IL_46306.1	1
85	IL_52958.1	1
86	IL_55934.1	1	kink-turn-like
87	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
88	IL_76486.1	1	Sarcin-ricin motif with syn G
89	IL_85805.1	1
90	IL_91078.1	1
91	IL_98924.1	1
92	IL_06306.1	1
93	IL_12233.1	1
94	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
95	IL_40845.1	1
96	IL_53323.1	1
97	IL_59529.1	1
98	IL_67735.1	1
99	IL_82113.1	1
100	IL_86059.1	1
101	IL_91089.1	1
102	IL_96260.1	1
103	IL_02690.1	1
104	IL_06468.1	1	16S h40 3WJ E.c.
105	IL_12486.1	1
106	IL_22579.1	1
107	IL_25181.1	1
108	IL_47687.1	1
109	IL_53988.1	1
110	IL_61723.1	1
111	IL_78809.1	1
112	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
113	IL_91904.1	1
114	IL_97073.1	1
115	IL_02835.1	1
116	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
117	IL_15205.1	1
118	IL_29949.1	1
119	IL_41009.1	1
120	IL_54450.1	1
121	IL_61730.1	1
122	IL_71685.1	1	Sarcin-like with an intercalated basepair
123	IL_92280.1	1
124	IL_02957.1	1
125	IL_07375.1	1
126	IL_22858.1	1
127	IL_25307.1	1
128	IL_30390.1	1
129	IL_37347.1	1
130	IL_41139.1	1
131	IL_54576.1	1
132	IL_62352.1	1
133	IL_71942.1	1
134	IL_82650.1	1
135	IL_88367.1	1
136	IL_97842.1	1

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_65553.2	21	Kink-turn
11	IL_32390.2	21	16S h19 IL and 23S H41 IL
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_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16	IL_31555.2	15	16S decoding site
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_27618.2	11	23S H73 ILa : Part of larger Motif
20	IL_40090.2	11	16S h34 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_92114.2	9	GAAA loop receptor "platform" motif
23	IL_58291.2	9	Recurrent Sub-motif found in junctions
24	IL_47444.2	9	SRP Loop E-like 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_73000.2	7	cHS-cWS
28	IL_86357.2	7	LSU Helix 61 IL2
29	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
30	IL_25230.2	6	Bacterial 5S rRNA Loop E
31	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
32	IL_97057.2	6
33	IL_70237.3	6
34	IL_53635.2	6	LSU Helix 32 (H32) IL
35	IL_72158.2	6	LSU Helix 62 (H62) IL
36	IL_13069.2	6	LSU 3WJ H32-H33-H35A
37	IL_24022.2	6
38	IL_02359.2	5
39	IL_45262.2	5
40	IL_79083.2	5
41	IL_78732.3	5	Double S-turn motif
42	IL_80179.2	5
43	IL_40387.2	5
44	IL_38807.2	4
45	IL_64184.2	4
46	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
47	IL_98591.2	4
48	IL_39526.2	4
49	IL_34156.2	3	cWW AG or UU
50	IL_23262.3	3
51	IL_80494.2	3	LSU H58 IL2 H.m.
52	IL_09348.2	3
53	IL_16252.2	3	23S H91 IL
54	IL_34628.2	3	Kink-turn
55	IL_58586.2	3
56	IL_82831.2	2	Kink-turn from 16S H23
57	IL_41397.2	2	LSU Helix 96 (H96) IL2
58	IL_76095.3	2	Motif from Hairpin Ribozyme
59	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS

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_11167.3	4
17	IL_49111.1	4	tHS tHH bulge with S-turn
18	IL_11594.1	4
19	IL_92333.1	4
20	IL_18947.1	4
21	IL_69124.1	4
22	IL_13740.1	3
23	IL_99434.1	3	Single-Base Intercalation Site
24	IL_30979.1	3
25	IL_10804.1	3
26	IL_19889.1	2
27	IL_75449.1	2
28	IL_92123.1	2
29	IL_67117.1	2
30	IL_68736.1	2
31	IL_02691.1	2
32	IL_44742.1	2
33	IL_57870.1	2
34	IL_88684.1	2
35	IL_09390.1	2
36	IL_47247.1	2
37	IL_69009.1	2
38	IL_89461.1	2
39	IL_62718.1	2
40	IL_19202.1	2
41	IL_63741.1	2
42	IL_91543.1	2
43	IL_38333.1	1
44	IL_65978.1	1
45	IL_24335.1	1
46	IL_39165.1	1
47	IL_50767.1	1
48	IL_39230.1	1
49	IL_67697.1	1
50	IL_55167.1	1
51	IL_14225.1	1
52	IL_29877.1	1
53	IL_99165.1	1
54	IL_17109.1	1
55	IL_30650.1	1
56	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
57	IL_91513.1	1
58	IL_31793.1	1	Kink-turn from 16S H23
59	IL_48650.1	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_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
5	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
7	IL_08926.1	6	23S H91 IL
8	IL_10007.1	6	Single sheared with bulged bases
9	IL_89088.1	6	16S h19 IL and 23S H41 IL
10	IL_07911.1	5
11	IL_77263.1	5	Kink-turn from U4
12	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
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_43946.1	3
17	IL_45808.1	3
18	IL_75447.1	3
19	IL_53774.1	3	Single sheared with bulged bases
20	IL_71565.1	3
21	IL_74291.1	2
22	IL_21495.1	2
23	IL_91026.1	2
24	IL_14023.1	2
25	IL_00998.1	2
26	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
27	IL_31707.1	2	Vitamin B12 aptamer
28	IL_78674.1	2	tHS tHH bulge with S-turn
29	IL_01054.1	2
30	IL_37406.1	2
31	IL_48285.1	2	Leadzyme Motif
32	IL_65137.1	2	Kink-turn like motif in Group I Intron
33	IL_12068.1	2
34	IL_87548.1	2
35	IL_99575.1	2
36	IL_12269.1	2
37	IL_43933.1	2
38	IL_12507.1	1
39	IL_56513.1	1
40	IL_89794.1	1
41	IL_07675.1	1	tHS tHH bulge with S-turn
42	IL_13682.1	1
43	IL_21421.1	1
44	IL_56779.1	1
45	IL_90880.1	1
46	IL_13942.1	1
47	IL_57977.1	1
48	IL_31241.1	1
49	IL_47457.1	1
50	IL_58454.1	1
51	IL_95939.1	1
52	IL_60643.1	1
53	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
54	IL_11869.1	1
55	IL_17603.1	1
56	IL_82601.1	1	Tandem cWW water-inserted CU pairs
57	IL_18755.1	1
58	IL_41849.1	1
59	IL_53423.1	1