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_82188.1	5	LSU H68 IL from H.m.
2	IL_92484.1	5
3	IL_01239.1	5
4	IL_22732.1	4	tSH-inserted-tHS
5	IL_31066.2	4	SSU Helix 44 (h44) extension
6	IL_28572.1	4	16S h18 kink-turn like motif
7	IL_37053.1	3	Kink-turn from 23S H58
8	IL_79955.2	3	SSU Helix (23) h23 IL1
9	IL_82563.1	3	Thi-box riboswitch T-loop
10	IL_15840.1	3
11	IL_52173.1	3
12	IL_30840.1	3
13	IL_62499.2	3
14	IL_98421.1	3
15	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
16	IL_95150.2	3
17	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
18	IL_34363.1	3	Kink-turn from 23S H42
19	IL_28942.1	2
20	IL_40892.1	2
21	IL_70280.1	2	Double sheared with wobble cWW.
22	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
23	IL_37197.1	2
24	IL_50521.1	2
25	IL_87173.1	2
26	IL_97833.1	2
27	IL_80093.1	2
28	IL_92459.1	2
29	IL_16166.1	2
30	IL_23414.1	2
31	IL_74876.1	2
32	IL_09882.1	2
33	IL_16330.1	2
34	IL_55287.1	2
35	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
36	IL_98566.1	2
37	IL_45794.1	2
38	IL_52940.1	2
39	IL_90057.1	2
40	IL_12211.1	2
41	IL_81441.1	2
42	IL_25174.1	2
43	IL_46435.1	2
44	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
45	IL_02690.1	1
46	IL_06468.1	1	16S h40 3WJ E.c.
47	IL_12486.1	1
48	IL_22579.1	1
49	IL_25181.1	1
50	IL_47687.1	1
51	IL_53988.1	1
52	IL_61723.1	1
53	IL_78809.1	1
54	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
55	IL_91904.1	1
56	IL_97073.1	1
57	IL_02835.1	1
58	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
59	IL_15205.1	1
60	IL_29949.1	1
61	IL_41009.1	1
62	IL_54450.1	1
63	IL_61730.1	1
64	IL_71685.1	1	Sarcin-like with an intercalated basepair
65	IL_92280.1	1
66	IL_02957.1	1
67	IL_07375.1	1
68	IL_22858.1	1
69	IL_25307.1	1
70	IL_30390.1	1
71	IL_37347.1	1
72	IL_41139.1	1
73	IL_54576.1	1
74	IL_62352.1	1
75	IL_71942.1	1
76	IL_82650.1	1
77	IL_88367.1	1
78	IL_97842.1	1
79	IL_03110.1	1
80	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
81	IL_25739.1	1	M-Box Riboswitch
82	IL_37715.1	1
83	IL_41791.1	1
84	IL_52509.1	1
85	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
86	IL_80505.1	1
87	IL_83250.1	1	16S h40 3WJ T.th.
88	IL_88403.1	1
89	IL_03741.1	1
90	IL_23639.1	1	tWH-tHS-L-cWW
91	IL_26241.1	1
92	IL_37990.1	1
93	IL_43316.1	1
94	IL_52752.1	1
95	IL_63952.1	1
96	IL_75415.1	1	Pseudo-knot forming internal loop
97	IL_80652.1	1
98	IL_83920.1	1
99	IL_05221.1	1
100	IL_11302.1	1
101	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
102	IL_24143.1	1	Yeast 18S
103	IL_26868.1	1
104	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
105	IL_39324.1	1
106	IL_55649.1	1
107	IL_65788.1	1
108	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
109	IL_81398.1	1
110	IL_85510.1	1
111	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
112	IL_05462.1	1
113	IL_20775.1	1	tSH-inserted
114	IL_25082.1	1
115	IL_26971.1	1
116	IL_32080.1	1
117	IL_40527.1	1	Kink-turn
118	IL_46306.1	1
119	IL_52958.1	1
120	IL_55934.1	1	kink-turn-like
121	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
122	IL_76486.1	1	Sarcin-ricin motif with syn G
123	IL_85805.1	1
124	IL_91078.1	1
125	IL_98924.1	1
126	IL_06306.1	1
127	IL_12233.1	1
128	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
129	IL_40845.1	1
130	IL_53323.1	1
131	IL_59529.1	1
132	IL_67735.1	1
133	IL_82113.1	1
134	IL_86059.1	1
135	IL_91089.1	1
136	IL_96260.1	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_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_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18	IL_94430.2	14	16S h32-h33-h34 3WJ
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_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_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
28	IL_73000.2	7	cHS-cWS
29	IL_86357.2	7	LSU Helix 61 IL2
30	IL_53635.2	6	LSU Helix 32 (H32) IL
31	IL_72158.2	6	LSU Helix 62 (H62) IL
32	IL_13069.2	6	LSU 3WJ H32-H33-H35A
33	IL_24022.2	6
34	IL_25230.2	6	Bacterial 5S rRNA Loop E
35	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36	IL_97057.2	6
37	IL_70237.3	6
38	IL_78732.3	5	Double S-turn motif
39	IL_80179.2	5
40	IL_40387.2	5
41	IL_02359.2	5
42	IL_45262.2	5
43	IL_79083.2	5
44	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45	IL_98591.2	4
46	IL_39526.2	4
47	IL_38807.2	4
48	IL_64184.2	4
49	IL_34628.2	3	Kink-turn
50	IL_58586.2	3
51	IL_34156.2	3	cWW AG or UU
52	IL_23262.3	3
53	IL_80494.2	3	LSU H58 IL2 H.m.
54	IL_09348.2	3
55	IL_16252.2	3	23S H91 IL
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_59016.1	5
12	IL_24476.1	5
13	IL_78157.1	5
14	IL_92936.1	5
15	IL_93335.2	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_99434.1	3	Single-Base Intercalation Site
23	IL_30979.1	3
24	IL_10804.1	3
25	IL_13740.1	3
26	IL_09390.1	2
27	IL_47247.1	2
28	IL_69009.1	2
29	IL_89461.1	2
30	IL_62718.1	2
31	IL_19202.1	2
32	IL_63741.1	2
33	IL_91543.1	2
34	IL_19889.1	2
35	IL_75449.1	2
36	IL_92123.1	2
37	IL_67117.1	2
38	IL_68736.1	2
39	IL_02691.1	2
40	IL_44742.1	2
41	IL_57870.1	2
42	IL_88684.1	2
43	IL_17109.1	1
44	IL_30650.1	1
45	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
46	IL_91513.1	1
47	IL_31793.1	1	Kink-turn from 16S H23
48	IL_48650.1	1
49	IL_38333.1	1
50	IL_65978.1	1
51	IL_24335.1	1
52	IL_39165.1	1
53	IL_50767.1	1
54	IL_39230.1	1
55	IL_67697.1	1
56	IL_55167.1	1
57	IL_14225.1	1
58	IL_29877.1	1
59	IL_99165.1	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_98556.1	4
14	IL_21333.1	4	tSH-tHW-bulge
15	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
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_01054.1	2
22	IL_37406.1	2
23	IL_48285.1	2	Leadzyme Motif
24	IL_65137.1	2	Kink-turn like motif in Group I Intron
25	IL_12068.1	2
26	IL_87548.1	2
27	IL_99575.1	2
28	IL_12269.1	2
29	IL_43933.1	2
30	IL_74291.1	2
31	IL_21495.1	2
32	IL_91026.1	2
33	IL_14023.1	2
34	IL_00998.1	2
35	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
36	IL_31707.1	2	Vitamin B12 aptamer
37	IL_78674.1	2	tHS tHH bulge with S-turn
38	IL_11869.1	1
39	IL_17603.1	1
40	IL_82601.1	1	Tandem cWW water-inserted CU pairs
41	IL_18755.1	1
42	IL_41849.1	1
43	IL_53423.1	1
44	IL_12507.1	1
45	IL_56513.1	1
46	IL_89794.1	1
47	IL_07675.1	1	tHS tHH bulge with S-turn
48	IL_13682.1	1
49	IL_21421.1	1
50	IL_56779.1	1
51	IL_90880.1	1
52	IL_13942.1	1
53	IL_57977.1	1
54	IL_31241.1	1
55	IL_47457.1	1
56	IL_58454.1	1
57	IL_95939.1	1
58	IL_60643.1	1
59	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.