9EI2
Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to an apo RECQL5 helicase (RECQL5 IRI Module focused-classified)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0000428 | cellular_component | DNA-directed RNA polymerase complex |
| A | 0000974 | cellular_component | Prp19 complex |
| A | 0001172 | biological_process | RNA-templated transcription |
| A | 0003676 | molecular_function | nucleic acid binding |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003899 | molecular_function | DNA-directed RNA polymerase activity |
| A | 0003968 | molecular_function | RNA-directed RNA polymerase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005665 | cellular_component | RNA polymerase II, core complex |
| A | 0005694 | cellular_component | chromosome |
| A | 0005730 | cellular_component | nucleolus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006353 | biological_process | DNA-templated transcription termination |
| A | 0006355 | biological_process | regulation of DNA-templated transcription |
| A | 0006366 | biological_process | transcription by RNA polymerase II |
| A | 0006368 | biological_process | transcription elongation by RNA polymerase II |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0010628 | biological_process | positive regulation of gene expression |
| A | 0016740 | molecular_function | transferase activity |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0016787 | molecular_function | hydrolase activity |
| A | 0019900 | molecular_function | kinase binding |
| A | 0031625 | molecular_function | ubiquitin protein ligase binding |
| A | 0033120 | biological_process | positive regulation of RNA splicing |
| A | 0034062 | molecular_function | 5'-3' RNA polymerase activity |
| A | 0042789 | biological_process | mRNA transcription by RNA polymerase II |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050436 | molecular_function | microfibril binding |
| A | 1990841 | molecular_function | promoter-specific chromatin binding |
| U | 0000166 | molecular_function | nucleotide binding |
| U | 0000278 | biological_process | mitotic cell cycle |
| U | 0000724 | biological_process | double-strand break repair via homologous recombination |
| U | 0000993 | molecular_function | RNA polymerase II complex binding |
| U | 0003677 | molecular_function | DNA binding |
| U | 0003678 | molecular_function | DNA helicase activity |
| U | 0004386 | molecular_function | helicase activity |
| U | 0005524 | molecular_function | ATP binding |
| U | 0005634 | cellular_component | nucleus |
| U | 0005654 | cellular_component | nucleoplasm |
| U | 0005657 | cellular_component | replication fork |
| U | 0005694 | cellular_component | chromosome |
| U | 0005737 | cellular_component | cytoplasm |
| U | 0005829 | cellular_component | cytosol |
| U | 0006259 | biological_process | DNA metabolic process |
| U | 0006260 | biological_process | DNA replication |
| U | 0006281 | biological_process | DNA repair |
| U | 0006974 | biological_process | DNA damage response |
| U | 0009378 | molecular_function | four-way junction helicase activity |
| U | 0010605 | biological_process | negative regulation of macromolecule metabolic process |
| U | 0016787 | molecular_function | hydrolase activity |
| U | 0016853 | molecular_function | isomerase activity |
| U | 0016887 | molecular_function | ATP hydrolysis activity |
| U | 0034244 | biological_process | negative regulation of transcription elongation by RNA polymerase II |
| U | 0043138 | molecular_function | 3'-5' DNA helicase activity |
| U | 0045934 | biological_process | negative regulation of nucleobase-containing compound metabolic process |
| U | 0046872 | molecular_function | metal ion binding |
| U | 0051301 | biological_process | cell division |
| U | 0051304 | biological_process | chromosome separation |
| U | 0071466 | biological_process | cellular response to xenobiotic stimulus |
| U | 0072757 | biological_process | cellular response to camptothecin |
| U | 0097550 | cellular_component | transcription preinitiation complex |
| U | 0140097 | molecular_function | catalytic activity, acting on DNA |
| U | 1990414 | biological_process | replication-born double-strand break repair via sister chromatid exchange |
| U | 1990506 | biological_process | mitotic DNA-templated DNA replication |
| U | 2000042 | biological_process | negative regulation of double-strand break repair via homologous recombination |
Functional Information from PROSITE/UniProt
| 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 | PS00690 |
| Number of Residues | 10 |
| Details | DEAH_ATP_HELICASE DEAH-box subfamily ATP-dependent helicases signature. SyLVVDEAHC |
| Chain | Residue | Details |
| U | SER152-CYS161 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 9 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:28100692, ECO:0007744|PDB:5LB3, ECO:0007744|PDB:5LB5, ECO:0007744|PDB:5LBA |
| Chain | Residue | Details |
| U | PHE26 | |
| U | SER28 | |
| U | LYS30 | |
| U | GLN34 | |
| U | GLY55 | |
| U | ALA56 | |
| U | GLY57 | |
| U | LYS58 | |
| U | SER59 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0007744|PDB:5LB5 |
| Chain | Residue | Details |
| U | PRO53 | |
| A | ASP495 | |
| A | CYS74 | |
| A | CYS81 | |
| A | HIS84 | |
| A | CYS111 | |
| A | CYS114 | |
| A | CYS154 | |
| A | CYS184 | |
| A | ASN493 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:28100692, ECO:0007744|PDB:5LB3, ECO:0007744|PDB:5LB5, ECO:0007744|PDB:5LB8, ECO:0007744|PDB:5LBA |
| Chain | Residue | Details |
| U | CYS411 | |
| U | CYS431 | |
| U | CYS434 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:28100692, ECO:0007744|PDB:5LB3, ECO:0007744|PDB:5LB5, ECO:0007744|PDB:5LBA |
| Chain | Residue | Details |
| U | CYS427 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:D4ACP5 |
| Chain | Residue | Details |
| U | SER488 | |
| A | SER217 | |
| A | SER1868 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| U | SER491 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine; by CDK1 => ECO:0000269|PubMed:28575661, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| U | SER727 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| U | SER815 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| U | THR839 | |
| A | THR1933 | |
| A | THR1863 | |
| A | THR1870 | |
| A | THR1877 | |
| A | THR1912 | |
| A | THR1915 | |
| A | THR1919 | |
| A | THR1926 | |
| A | THR1929 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | SER1843 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685 |
| Chain | Residue | Details |
| A | SER1845 | |
| A | SER1857 | |
| A | SER1861 | |
| A | SER1875 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P08775 |
| Chain | Residue | Details |
| A | SER1847 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| A | SER1849 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1850 | |
| A | SER1864 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | THR1854 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:26566685 |
| Chain | Residue | Details |
| A | LYS1859 | |
| A | LYS1866 | |
| A | LYS1873 | |
| A | LYS1887 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 5 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26566685 |
| Chain | Residue | Details |
| A | TYR1860 | |
| A | TYR1867 | |
| A | TYR1881 | |
| A | TYR1916 | |
| A | TYR1930 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | TYR1874 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1878 | |
| A | SER1882 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | THR1885 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P08775 |
| Chain | Residue | Details |
| A | THR1894 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| A | SER1896 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1899 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER1906 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 1 |
| Details | MOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P08775 |
| Chain | Residue | Details |
| A | LYS1908 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:16964243, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | TYR1909 | |
| A | TYR1923 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 3 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:26566685, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER1913 | |
| A | SER1920 | |
| 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 |
