8XRJ
RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei
Functional Information from PROSITE/UniProt
| site_id | PS00018 |
| Number of Residues | 13 |
| Details | EF_HAND_1 EF-hand calcium-binding domain. DNDPNDYVEqdDI |
| Chain | Residue | Details |
| C | ASP136-ILE148 |
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| c | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| b | GLY14-HIS18 |
| site_id | PS00115 |
| Number of Residues | 7 |
| Details | RNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA |
| Chain | Residue | Details |
| A | TYR1593-ALA1599 | |
| A | TYR1671-SER1677 | |
| A | TYR1678-SER1684 | |
| A | TYR1685-SER1691 | |
| A | TYR1692-SER1698 | |
| A | TYR1699-SER1705 | |
| A | TYR1706-SER1712 | |
| A | TYR1713-SER1719 | |
| A | TYR1720-SER1726 | |
| A | TYR1727-SER1733 | |
| A | TYR1734-SER1740 | |
| A | TYR1615-SER1621 | |
| A | TYR1741-ASN1747 | |
| A | TYR1748-ASN1754 | |
| A | TYR1755-SER1761 | |
| A | TYR1762-SER1768 | |
| A | TYR1769-ASN1775 | |
| A | TYR1776-ASN1782 | |
| A | TYR1783-SER1789 | |
| A | TYR1790-SER1796 | |
| A | TYR1797-SER1803 | |
| A | TYR1818-SER1824 | |
| A | TYR1622-SER1628 | |
| A | TYR1825-SER1831 | |
| A | TYR1839-SER1845 | |
| A | TYR1853-LYS1859 | |
| A | TYR1860-LYS1866 | |
| A | TYR1867-LYS1873 | |
| A | TYR1874-THR1880 | |
| A | TYR1888-THR1894 | |
| A | TYR1902-LYS1908 | |
| A | TYR1909-THR1915 | |
| A | TYR1916-LYS1922 | |
| A | TYR1629-ASN1635 | |
| A | TYR1923-THR1929 | |
| A | TYR1930-LYS1936 | |
| A | TYR1947-THR1953 | |
| A | TYR1636-SER1642 | |
| A | TYR1643-SER1649 | |
| A | TYR1650-SER1656 | |
| A | TYR1657-SER1663 | |
| A | TYR1664-SER1670 |
| site_id | PS00290 |
| Number of Residues | 7 |
| Details | IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YVCTAPH |
| Chain | Residue | Details |
| I | TYR112-HIS118 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| a | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| d | ARG92-GLY114 |
| site_id | PS00446 |
| Number of Residues | 41 |
| Details | RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSIRRvfiaevpiiAidwVqidaNsSvlhDEfIAhRLGLIP |
| Chain | Residue | Details |
| C | ASN32-PRO72 |
| site_id | PS00466 |
| Number of Residues | 38 |
| Details | ZF_TFIIS_1 Zinc finger TFIIS-type signature. CqkCghkeavffqSHSARaEDAmrlyyvCtaph.CghrW |
| Chain | Residue | Details |
| I | CYS86-TRP123 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| a | PRO66-ILE74 |
| site_id | PS01030 |
| Number of Residues | 27 |
| Details | RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCQECNNMLypkedkenrillyaCrnC |
| Chain | Residue | Details |
| I | PHE16-CYS42 |
| site_id | PS01110 |
| Number of Residues | 14 |
| Details | RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPEHvvMtkEE |
| Chain | Residue | Details |
| E | HIS142-GLU155 |
| site_id | PS01111 |
| Number of Residues | 15 |
| Details | RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARvLGtRAlQ |
| Chain | Residue | Details |
| F | THR58-GLN72 |
| site_id | PS01112 |
| Number of Residues | 10 |
| Details | RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IIPVrCFTCG |
| Chain | Residue | Details |
| J | ILE2-GLY11 |
| site_id | PS01154 |
| Number of Residues | 32 |
| Details | RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. InkEdHTLgNiIksqLlkdpqVlfagYkvpHP |
| Chain | Residue | Details |
| K | ILE35-PRO66 |
| site_id | PS01166 |
| Number of Residues | 13 |
| Details | RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT |
| Chain | Residue | Details |
| B | GLY932-THR944 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 25 |
| Details | ZN_FING: C4-type => ECO:0000255 |
| Chain | Residue | Details |
| I | CYS17-CYS42 | |
| C | CYS90 | |
| C | CYS94 | |
| C | CYS97 | |
| A | ASP499 | |
| A | ARG1416 | |
| A | ARG1421 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 42 |
| Details | ZN_FING: TFIIS-type => ECO:0000255|PROSITE-ProRule:PRU00472 |
| Chain | Residue | Details |
| I | GLU82-THR124 | |
| A | ASP495 | |
| B | ASP792 | |
| A | CYS81 | |
| A | HIS84 | |
| A | CYS111 | |
| A | CYS114 | |
| A | CYS154 | |
| A | CYS184 | |
| A | ASN493 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU10145, ECO:0000269|PubMed:27193682, ECO:0007744|PDB:5IY6 |
| Chain | Residue | Details |
| I | CYS17 | |
| h | LYS11 | |
| h | LYS15 | |
| h | LYS16 | |
| h | LYS20 | |
| h | LYS23 | |
| h | LYS43 | |
| h | LYS85 | |
| I | CYS20 | |
| I | CYS39 | |
| I | CYS42 | |
| B | LYS942 | |
| B | ARG1078 | |
| B | ARG1085 | |
| d | LYS85 | |
| h | LYS5 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00472, ECO:0000269|PubMed:27193682, ECO:0007744|PDB:5IY6 |
| Chain | Residue | Details |
| I | CYS86 | |
| I | CYS89 | |
| I | CYS114 | |
| I | CYS119 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: N-acetylmethionine => ECO:0007744|PubMed:22814378 |
| Chain | Residue | Details |
| I | MET1 | |
| h | LYS12 | |
| b | LYS44 | |
| f | LYS8 | |
| f | LYS16 | |
| f | LYS44 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | MOD_RES: N6-methyllysine => ECO:0007744|PubMed:24129315 |
| Chain | Residue | Details |
| B | LYS1052 | |
| h | SER14 | |
| b | LYS77 | |
| b | LYS91 | |
| f | LYS12 | |
| f | LYS31 | |
| f | LYS77 | |
| f | LYS91 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537 |
| Chain | Residue | Details |
| d | LYS24 | |
| h | LYS24 | |
| g | LYS74 | |
| g | LYS75 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435 |
| Chain | Residue | Details |
| d | LYS34 | |
| d | LYS116 | |
| d | LYS120 | |
| h | LYS34 | |
| h | LYS116 | |
| h | LYS120 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475 |
| Chain | Residue | Details |
| d | GLU35 | |
| A | THR1933 | |
| h | GLU35 | |
| c | LYS125 | |
| g | LYS118 | |
| g | LYS119 | |
| g | LYS125 | |
| A | THR1919 | |
| A | THR1926 | |
| A | THR1929 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475 |
| Chain | Residue | Details |
| d | SER36 | |
| h | SER36 | |
| e | LYS14 | |
| e | LYS56 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869 |
| Chain | Residue | Details |
| d | LYS46 | |
| d | LYS108 | |
| h | LYS46 | |
| h | LYS108 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537 |
| Chain | Residue | Details |
| d | LYS57 | |
| h | LYS57 | |
| e | LYS18 | |
| g | LYS119 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08 |
| Chain | Residue | Details |
| d | ARG79 | |
| h | ARG79 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08 |
| Chain | Residue | Details |
| d | ARG86 | |
| d | ARG92 | |
| h | ARG86 | |
| h | ARG92 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729 |
| Chain | Residue | Details |
| d | THR115 | |
| h | THR115 | |
| f | LYS91 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
| Chain | Residue | Details |
| d | SER112 | |
| h | SER112 | |
| b | LYS79 | |
| f | LYS20 | |
| f | LYS59 | |
| f | LYS79 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876 |
| Chain | Residue | Details |
| d | LYS5 | |
| h | LYS5 | |
| A | TYR1881 | |
| A | TYR1916 | |
| A | TYR1930 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563 |
| Chain | Residue | Details |
| a | LYS37 | |
| d | LYS120 | |
| h | LYS120 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6 |
| Chain | Residue | Details |
| d | LYS20 | |
| h | LYS20 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816 |
| Chain | Residue | Details |
| d | LYS34 | |
| h | LYS34 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711 |
| Chain | Residue | Details |
| a | LYS79 | |
| e | LYS79 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016 |
| Chain | Residue | Details |
| a | THR80 | |
| e | THR80 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| a | SER86 | |
| e | SER86 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| a | THR107 | |
| e | THR107 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297 |
| Chain | Residue | Details |
| a | LYS115 | |
| e | LYS115 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229 |
| Chain | Residue | Details |
| a | LYS122 | |
| e | LYS122 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 2 |
| Details | LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806 |
| Chain | Residue | Details |
| a | LYS18 | |
| e | LYS18 | |
| A | SER1927 |
| site_id | SWS_FT_FI28 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| A | SER1917 | |
| A | SER1931 |
| site_id | SWS_FT_FI29 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000305|PubMed:26566685 |
| Chain | Residue | Details |
| A | LYS1922 | |
| A | LYS1936 |
| site_id | SWS_FT_FI30 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1934 |
| site_id | SWS_FT_FI31 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); by NEDD4 => ECO:0000269|PubMed:32142649, ECO:0000305|PubMed:32142654 |
| Chain | Residue | Details |
| A | LYS1268 |
