ars.els-cdn.com · Web viewEvaluation of 3D structure of hn/hm_RBP4. (A) Verify 3D result showed...
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Identification of RBP4 from bighead carp (Hypophthalmichthys nobilis) / silver carp (Hypophthalmichthys molitrix) and effects of CpG ODN on RBP4 expression under A. hydrophila challenge Jiaoqing Li a$, Qin Fan a$, Haiming Cai a$, Jinbo Deng a, Feiping Ming a, Jiayi Li a, Min Zeng a, Miaopeng Ma a, Peijing Zhao a, Qianyi Liang a, Junhao Jia a, Shuxia Zhang a, Linghua Zhang a,b * a Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China b Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
Transcript of ars.els-cdn.com · Web viewEvaluation of 3D structure of hn/hm_RBP4. (A) Verify 3D result showed...
Identification of RBP4 from bighead carp (Hypophthalmichthys
nobilis) / silver carp (Hypophthalmichthys molitrix) and effects
of CpG ODN on RBP4 expression under A. hydrophila
challenge
Jiaoqing Li a$, Qin Fan a$, Haiming Cai a$, Jinbo Deng a, Feiping Ming a, Jiayi Li a, Min Zeng a, Miaopeng Ma a, Peijing Zhao a, Qianyi Liang a, Junhao Jia a, Shuxia Zhang a, Linghua Zhang a,b *
a Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural
University, Guangzhou, Guangdong 510642, Chinab Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
*Corresponding author. E-mail address: [email protected] （LZ）$ These authors contributed equally to this work.
A
B
Figure S1. Subcellular localization (in percentage) of hn/hm_RBP4 protein in a different section of the cell. (A). Interaction networking between RBP4 and other proteins (B). The network was predicted by online software STRING
A.
B.
Figure S2. The analysis of RBP4 structural. (A) Secondary structure conducted by PSIPRED Protein Sequence Analysis Workbench for hn/hm_RBP4. (B) The 3-D structures of hn/hm_RBP4 conducted by ROBETTA based on the template 5nu7 (human RBP4 protein structure), displayed
by Chimera 1.13rc. Purple: α-helices; Green: random coils; Yellow: anti-parallel β–sheets.
A
B
C
D
Figure S3. Evaluation of 3D structure of hn/hm_RBP4. (A) Verify 3D result showed that 99.43% of the residues have averaged 3D-1D score >= 0.2. (B) ERRAT result showed that structure had 99.3827 quality factor. (C) Ramachandran plot for hn/hm_RBP4 structure also showed that the structure shared a good structural stereochemistry. (D) Prosa result showed that it had a -6.63 Z-score.
NO.Accession
no.Species 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
1NP_570995.1
D. rerio53.
5
59.
1
55.
7
57.
3
54.
755
57.
9
53.
5
54.
2
82.
3
82.
8
79.
2
79.
7
92.
2
54.
7
74.
288
76.
6
55.
7
73.
4
56.
8
55.
7
90.
1
2NP_035385.1
M. musculus73.
6
72.
1
86.
158
84.
6
86.
1
57.
1
99.
5
85.
1
56.
2
55.
4
54.
2
53.
554
83.
1
57.
953 53
83.
655
79.
8
92.
5
53.
5
3NP_990569.1
G. gallus77.
6
86.
6
76.
5
59.
2
75.
576
61.
3
72.
1
75.
5
60.
1
59.
6
59.
6
59.
6
58.
6
78.
4
58.
8
58.
6
56.
1
75.
5
60.
6
76.
5
74.
5
57.
6
4NP_999222.1
S. scrofa73.
1
92.
5
88.
1
57.
1
93.
5
90.
5
58.
1
85.
696
57.
2
56.
7
55.
2
53.
7
55.
7
93.
5
59.
4
55.
2
53.
7
95.
5
56.
9
86.
2
86.
1
55.
2
5NP_0010754
20.1X. tropicalis
69.
8
77.
6
78.
4
75.
6
56.
459
83.
458
57.
6
52.
3
52.
3
52.
3
52.
856 59
53.
2
51.
8
50.
358 52
55.
458
53.
8
6NP_0010754
20.1E. caballus
75.
192
88.
1
97.
5
75.
6
89.
6
58.
6
84.
693
56.
7
56.
2
55.
2
54.
2
56.
293
58.
9
55.
9
53.
793
55.
9
87.
2
85.
6
55.
9
7NP_0010757
90.1O. cuniculus
74.
692
89.
196
75.
6
96.
5
57.
6
86.
192
55.
7
55.
4
53.
7
53.
5
56.
491
58.
4
55.
4
53.
591
56.
4
84.
7
87.
1
55.
4
8NP_0010811
95.1X.laevis
72.
6
78.
1
82.
2
78.
1
91.
5
78.
1
78.
1
57.
1
58.
1
54.
8
54.
8
54.
8
55.
3
55.
3
58.
1
56.
4
53.
8
52.
8
58.
6
55.
6
57.
6
58.
1
54.
3
9NP_037294.1
R.norvegicus73.
6100
86.
6
92.
5
77.
692 92
78.
1
84.
6
56.
2
55.
4
54.
2
53.
554
83.
1
57.
953 53
83.
655
79.
893
53.
5
10NP_0010355
65.2B.taurus
74.
6
92.
5
89.
198
76.
198
96.
5
78.
1
92.
5
56.
2
55.
7
53.
7
53.
7
55.
2
93.
5
58.
455
53.
2
98.
5
56.
4
85.
2
86.
6
55.
9
11NP_0011177
50.1O.mykiss
90.
6
75.
6
78.
6
75.
6
70.
4
76.
6
75.
6
74.
1
75.
6
76.
6
98.
4
85.
9
85.
4
82.
8
56.
7
76.
3
82.
388
57.
2
77.
1
56.
8
57.
7
82.
3
12NP_0011342
45.1S.salar
91.
1
75.
1
78.
6
74.
6
70.
4
75.
6
75.
6
74.
1
75.
1
75.
6
99.
5
85.
4
84.
9
83.
3
56.
2
75.
8
82.
888
56.
7
76.
6
56.
8
57.
2
82.
8
13ACO09874.1
O.mordax89.
1
74.
1
77.
6
74.
1
69.
3
75.
6
73.
6
72.
6
74.
1
74.
6
91.
1
91.
7
92.
7
79.
2
54.
2
73.
7
78.
6
78.
6
54.
2
72.
9
54.
3
55.
7
78.
6
14CAY66442.1
P.altivelis89.
6
73.
6
78.
1
73.
1
71.
4
74.
6
74.
1
73.
6
73.
6
74.
6
92.
7
93.
2
95.
3
78.
6
53.
7
75.
3
78.
1
80.
2
54.
275
53.
8
55.
2
78.
1
15AGS58251.1
C.batrachus96.
9
72.
6
76.
5
73.
1
68.
8
73.
6
73.
6
71.
6
72.
6
73.
6
90.
6
90.
6
89.
6
89.
6
55.
7
72.
7
93.
2
77.
6
56.
2
70.
3
57.
3
56.
2
95.
3
16NP_0012771
78.1F.catus
74.
191 90 97
78.
1
97.
597
78.
691 98
76.
1
75.
1
74.
1
73.
6
73.
1
57.
2
55.
2
53.
2
93.
5
56.
4
87.
2
85.
1
55.
2
17AII25441.1
T.ovatus82.
3
77.
1
78.
3
78.
1
69.
8
78.
6
78.
1
72.
7
77.
1
79.
1
85.
4
85.
9
83.
3
85.
4
81.
8
76.
6
71.
2
73.
2
58.
9
79.
3
57.
8
60.
4
72.
2
18AIU34720.1
M.amblycep
hala
97.
4
72.
6
77.
6
72.
6
69.
8
73.
6
74.
1
71.
6
72.
6
74.
1
90.
6
90.
1
89.
1
89.
699
72.
6
82.
3
78.
1
55.
7
70.
8
56.
8
55.
2
95.
8
19NP_0012978
79.1E.lucius
88.
5
71.
6
74.
5
71.
6
67.
8
72.
6
72.
1
71.
6
71.
6
72.
6
93.
8
94.
388
90.
1
89.
1
71.
6
83.
888
54.
275
53.
8
54.
7
76.
6
20NP_0013011
58.1C.hircus
74.
692
88.
1
97.
5
76.
1
97.
596
78.
1
91.
5
99.
5
77.
1
76.
1
74.
6
74.
6
74.
1
97.
5
79.
1
73.
6
73.
1
56.
9
85.
7
85.
6
56.
7
21AMT85041.1
E.coioides85.
9
75.
6
79.
1
76.
1
70.
4
77.
6
76.
6
73.
1
75.
6
77.
6
86.
587
84.
987
84.
4
77.
1
89.
9
84.
9
85.
4
77.
6
55.
3
57.
4
69.
8
22NP_0013104
47.1H.sapiens
73.
9
87.
6
86.
9
91.
5
75.
4
92.
5
92.
5
77.
4
87.
6
92.
5
75.
9
75.
4
73.
9
73.
9
72.
993
76.
4
72.
4
71.
9
92.
5
74.
9
79.
8
56.
8
23APD32941.1
C.fiber76.
1
95.
5
88.
693
77.
1
93.
5
93.
5
78.
1
95.
5
94.
5
79.
1
78.
1
76.
6
76.
1
74.
693
81.
1
74.
6
74.
6
93.
5
79.
1
89.
1
55.
2
24 H.nobilis96.
9
73.
177
72.
6
69.
8
74.
1
74.
1
72.
1
73.
1
74.
1
90.
1
89.
6
88.
5
89.
1
98.
4
73.
1
82.
3
99.
5
87.
5
73.
6
84.
4
72.
9
74.
1
25 H.molitrix96.
9
73.
177
72.
6
69.
8
74.
1
74.
1
72.
1
73.
1
74.
1
90.
1
89.
6
88.
5
89.
1
98.
4
73.
1
82.
3
99.
5
87.
5
73.
6
84.
4
72.
9
74.
1100
Table S1. The similarities of amino acid sequences between Hypophthalmichthys molitrix (or Hypophthalmichthys nobilis) and other animals.
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