Table 1. LC-MS/MS identification of proteins pulled-down with HCV CRE.
| Protein name | Name | Accession | M | P | U.P | Cov. | Ratio | HCV gen. | Ref. |
|---|---|---|---|---|---|---|---|---|---|
| 40S ribosomal protein SA (Fragment) | RPSA | C9J9K3 | 30 | 3 | 3 | 15.00 | 1.00 : 0.35 | IRES | 61 |
| Actin. cytoplasmic 1 | ACTB | P60709 | 42 | 21 | 4 | 40.18 | 1.00 : 0.34 | ||
| Activated RNA polymerase II transcriptional coactivator p15 | SUB1 | P53999 | 14 | 10 | 10 | 43.31 | 1.00 : 0.02 | 3′UTR | 26 |
| Alpha-enolase | ENO1 | P06733 | 47 | 6 | 4 | 16.53 | 1.00 : 0.06 | ||
| AT-rich interactive domain-containing protein 3A | ARID3A | Q99856 | 63 | 9 | 8 | 14.45 | 1.00 : 0.20 | ||
| Bifunctional polynucleotide phosphatase/kinase | PNKP | Q96T60 | 57 | 22 | 19 | 38.10 | 1.00 : 0.01 | ||
| Cellular nucleic acid-binding protein (isoform 2) | CNBP | P62633-2 | 19 | 7 | 6 | 35.68 | 1.00 : 0.04 | ||
| DAZ-associated protein 1 | DAZPA1 | Q96EP5 | 43 | 6 | 5 | 18.42 | 1.00 : 0.05 | ||
| DNA ligase 3 | LIG3 | P49916 | 113 | 17 | 13 | 16.60 | 1.00 : 0.04 | ||
| DNA polymerase beta | POLB | P06746 | 38 | 8 | 7 | 24.25 | 1.00 : 0.01 | 3′UTR | 26 |
| DNA repair protein XRCC1 | XRCC1 | P18887 | 69 | 20 | 17 | 24.76 | 1.00 : 0.02 | ||
| DNA-(apurinic or apyrimidinic site) lyase | APEX1 | P27695 | 36 | 5 | 4 | 19.81 | 1.00 : 0.00 | ||
| Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein | HMCES | Q96FZ2 | 41 | 9 | 9 | 27.68 | 1.00 : 0.03 | ||
| Eukaryotic translation initiation factor 3 subunit I | EIF3I | Q13347 | 37 | 5 | 4 | 17.00 | 1.00 : 0.21 | ||
| Exosome complex component RRP41 | EXOSC4 | Q9NPD3 | 26 | 5 | 4 | 20.91 | 1.00 : 0.04 | ||
| Far upstream element-binding protein 3 | FUBP3 | Q96I24 | 62 | 7 | 6 | 14.90 | 1.00 : 0.28 | ||
| Fructose-bisphosphate aldolase A | ALDOA | P04075 | 39 | 7 | 6 | 18.04 | 1.00 : 0.11 | ||
| Glyceraldehyde-3-phosphate dehydrogenase | GAPDH | P04406 | 36 | 9 | 8 | 23.78 | 1.00 : 0.05 | 3′UTR | 26 |
| Helicase-like transcription factor | HLTF | Q14527 | 114 | 27 | 25 | 22.94 | 1.00 : 0.04 | ||
| Heterogeneous nuclear ribonucleoprotein A/B | HNRNPAB | D6RD18 | 30 | 5 | 4 | 21.27 | 1.00 : 0.02 | ||
| Heterogeneous nuclear ribonucleoprotein A0 | HNRNPA0 | Q13151 | 31 | 9 | 8 | 26.88 | 1.00 : 0.03 | IRES | 61 |
| Heterogeneous nuclear ribonucleoprotein A1 | HNRNPA1 | F8W6I7 | 33 | 30 | 16 | 53.58 | 1.00 : 0.03 | 3′UTR IRES | 26 48 61 |
| Heterogeneous nuclear ribonucleoprotein A3 | HNRNPA3 | P51991 | 40 | 19 | 17 | 34.92 | 1.00 : 0.02 | ||
| Heterogeneous nuclear ribonucleoprotein D-like (isoform 3) | HNRNPDL | O14979-3 | 28 | 5 | 4 | 22.75 | 1.00 : 0.06 | 3′UTR IRES | 26 61 |
| Heterogeneous nuclear ribonucleoprotein M (isoform 2) | HNRNPM | P52272-2 | 74 | 65 | 14 | 50.28 | 1.00 : 0.11 | ||
| Heterogeneous nuclear ribonucleoprotein U | HNRNPU | Q00839 | 91 | 24 | 21 | 21.72 | 1.00 : 0.08 | 3′UTR | 26 |
| Heterogeneous nuclear ribonucleoproteins A2/B1 | HNRNPA2B1 | P22626 | 37 | 20 | 17 | 39.94 | 1.00 : 0.04 | ||
| High mobility group protein B1 | HMGB1 | P09429 | 25 | 9 | 5 | 36.51 | 1.00 : 0.01 | IRES | 61 |
| High mobility group protein B2 | HMGB2 | P26583 | 24 | 14 | 11 | 41.63 | 1.00 : 0.02 | ||
| Isocitrate dehydrogenase [NADP] cytoplasmic | IDH1 | O75874 | 47 | 19 | 16 | 39.37 | 1.00 : 0.27 | ||
| Lamina-associated polypeptide 2. isoform alpha | TMPO | P42166 | 75 | 9 | 6 | 16.85 | 1.00 : 0.08 | ||
| L-lactate dehydrogenase A chain | LDHA | P00338 | 37 | 11 | 9 | 31.70 | 1.00 : 0.18 | ||
| Poly [ADP-ribose] polymerase 1 | PARP1 | P09874 | 113 | 53 | 51 | 36.61 | 1.00 : 0.02 | 3′UTR | 26 |
| Probable ATP-dependent RNA helicase DDX5 | DDX5 | P17844 | 69 | 8 | 6 | 15.06 | 1.00 : 0.30 | 3′UTR | 26 |
| Proteasome subunit alpha type-1 | PSMA1 | P25786 | 30 | 4 | 3 | 18.72 | 1.00 : 0.14 | ||
| Putative RNA-binding protein 3 | RBM3 | P98179 | 17 | 7 | 7 | 36.94 | 1.00 : 0.04 | IRES | 61 |
| Ras GTPase-activating protein-binding protein 1 | G3BP1 | Q13283 | 52 | 13 | 12 | 26.10 | 1.00 : 0.31 | ||
| Ras GTPase-activating protein-binding protein 2 (isoform B) | G3BP2 | Q9UN86-2 | 51 | 10 | 9 | 17.87 | 1.00 : 0.11 | ||
| Replication protein A 14 kDa subunit | RPA3 | P35244 | 14 | 3 | 3 | 31.33 | 1.00 : 0.02 | ||
| Replication protein A 32 kDa subunit (isoform 3) | RPA2 | P15927-3 | 39 | 6 | 5 | 16.11 | 1.00 : 0.00 | ||
| Replication protein A 70 kDa DNA-binding subunit | RPA1 | P27694 | 68 | 24 | 19 | 31.69 | 1.00 : 0.02 | ||
| RNA-binding motif. single-stranded-interacting protein 1 | RBMS1 | E7ETU5 | 46 | 5 | 5 | 16.80 | 1.00 : 0.05 | ||
| RNA-binding protein 7 | RBM7 | Q9Y580 | 31 | 5 | 4 | 17.01 | 1.00 : 0.02 | ||
| RNA-binding protein Musashi homolog 1 | MSI1 | O43347 | 39 | 7 | 5 | 18.32 | 1.00 : 0.04 | ||
| RNA-binding protein Musashi homolog 2 (isoform 2) | MSI2 | Q96DH6-2 | 28 | 11 | 8 | 34.66 | 1.00 : 0.04 | IRES | 61 |
| Single-stranded DNA-binding protein (Fragment) | SSBP1 | E7EUY5 | 16 | 3 | 3 | 27.74 | 1.00 : 0.14 | IRES | 61 |
| Splicing factor. proline- and glutamine-rich | SFPQ | P23246 | 76 | 14 | 13 | 19.48 | 1.00 : 0.29 | 3′UTR | 26 |
| T-complex protein 1 subunit theta | CCT8 | P50990 | 60 | 13 | 12 | 25.59 | 1.00 : 0.25 | ||
| Thymidylate kinase | DTYMK | P23919 | 24 | 7 | 4 | 30.50 | 1.00 : 0.02 | ||
| Transcriptional activator protein Pur-beta | PURB | Q96QR8 | 33 | 5 | 4 | 16.26 | 1.00 : 0.04 | ||
| X-ray repair cross-complementing protein 5 | XRCC5 | P13010 | 83 | 24 | 22 | 26.74 | 1.00 : 0.15 | ||
| X-ray repair cross-complementing protein 6 | XRCC6 | P12956 | 70 | 29 | 28 | 35.22 | 1.00 : 0.15 | 3′UTR IRES | 26 61 |
| YTH domain family protein 1 | YTHDF1 | Q9BYJ9 | 61 | 14 | 5 | 25.51 | 1.00 : 0.09 | ||
| YTH domain family protein 2 | YTHDF2 | Q9Y5A9 | 62 | 14 | 10 | 25.82 | 1.00 : 0.11 | ||
| YTH domain family protein 3 | YTHDF3 | Q7Z739 | 64 | 18 | 7 | 32.88 | 1.00 : 0.10 |
Name, gene name; Accession, Uniprot accession number; M, molecular mass (kDa); P, number of peptides identified in the positive samples; U.P, number of unique peptides identified in the positive samples; Cov., coverage of full-length protein in positive samples by tryptic peptides (%); Ratio, average of peak area ratios from peptides in positive samples; compared to control samples; HCV gen., other reported HCV genome domains which associate with the protein; Ref., references for the named interactions.