8U5H
Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| I | 0000776 | cellular_component | kinetochore |
| I | 0000786 | cellular_component | nucleosome |
| I | 0003677 | molecular_function | DNA binding |
| I | 0005634 | cellular_component | nucleus |
| I | 0005694 | cellular_component | chromosome |
| I | 0007080 | biological_process | mitotic metaphase chromosome alignment |
| I | 0030527 | molecular_function | structural constituent of chromatin |
| I | 0031492 | molecular_function | nucleosomal DNA binding |
| I | 0031507 | biological_process | heterochromatin formation |
| I | 0046982 | molecular_function | protein heterodimerization activity |
| I | 0051382 | biological_process | kinetochore assembly |
| J | 0000786 | cellular_component | nucleosome |
| J | 0003677 | molecular_function | DNA binding |
| J | 0005515 | molecular_function | protein binding |
| J | 0005634 | cellular_component | nucleus |
| J | 0005694 | cellular_component | chromosome |
| J | 0006334 | biological_process | nucleosome assembly |
| J | 0030527 | molecular_function | structural constituent of chromatin |
| J | 0031507 | biological_process | heterochromatin formation |
| J | 0046982 | molecular_function | protein heterodimerization activity |
| K | 0000786 | cellular_component | nucleosome |
| K | 0003677 | molecular_function | DNA binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0005694 | cellular_component | chromosome |
| K | 0030527 | molecular_function | structural constituent of chromatin |
| K | 0031507 | biological_process | heterochromatin formation |
| K | 0046982 | molecular_function | protein heterodimerization activity |
| M | 0000786 | cellular_component | nucleosome |
| M | 0002227 | biological_process | innate immune response in mucosa |
| M | 0003677 | molecular_function | DNA binding |
| M | 0005515 | molecular_function | protein binding |
| M | 0005615 | cellular_component | extracellular space |
| M | 0005634 | cellular_component | nucleus |
| M | 0005694 | cellular_component | chromosome |
| M | 0006325 | biological_process | chromatin organization |
| M | 0019731 | biological_process | antibacterial humoral response |
| M | 0030527 | molecular_function | structural constituent of chromatin |
| M | 0031507 | biological_process | heterochromatin formation |
| M | 0046982 | molecular_function | protein heterodimerization activity |
| M | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| O | 0000776 | cellular_component | kinetochore |
| O | 0000786 | cellular_component | nucleosome |
| O | 0003677 | molecular_function | DNA binding |
| O | 0005634 | cellular_component | nucleus |
| O | 0005694 | cellular_component | chromosome |
| O | 0007080 | biological_process | mitotic metaphase chromosome alignment |
| O | 0030527 | molecular_function | structural constituent of chromatin |
| O | 0031492 | molecular_function | nucleosomal DNA binding |
| O | 0031507 | biological_process | heterochromatin formation |
| O | 0046982 | molecular_function | protein heterodimerization activity |
| O | 0051382 | biological_process | kinetochore assembly |
| Q | 0000786 | cellular_component | nucleosome |
| Q | 0003677 | molecular_function | DNA binding |
| Q | 0005515 | molecular_function | protein binding |
| Q | 0005634 | cellular_component | nucleus |
| Q | 0005694 | cellular_component | chromosome |
| Q | 0006334 | biological_process | nucleosome assembly |
| Q | 0030527 | molecular_function | structural constituent of chromatin |
| Q | 0031507 | biological_process | heterochromatin formation |
| Q | 0046982 | molecular_function | protein heterodimerization activity |
| R | 0000786 | cellular_component | nucleosome |
| R | 0003677 | molecular_function | DNA binding |
| R | 0005634 | cellular_component | nucleus |
| R | 0005694 | cellular_component | chromosome |
| R | 0030527 | molecular_function | structural constituent of chromatin |
| R | 0031507 | biological_process | heterochromatin formation |
| R | 0046982 | molecular_function | protein heterodimerization activity |
| S | 0000786 | cellular_component | nucleosome |
| S | 0002227 | biological_process | innate immune response in mucosa |
| S | 0003677 | molecular_function | DNA binding |
| S | 0005515 | molecular_function | protein binding |
| S | 0005615 | cellular_component | extracellular space |
| S | 0005634 | cellular_component | nucleus |
| S | 0005694 | cellular_component | chromosome |
| S | 0006325 | biological_process | chromatin organization |
| S | 0019731 | biological_process | antibacterial humoral response |
| S | 0030527 | molecular_function | structural constituent of chromatin |
| S | 0031507 | biological_process | heterochromatin formation |
| S | 0046982 | molecular_function | protein heterodimerization activity |
| S | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| K | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| J | GLY14-HIS18 |
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| D | LYS27-ASP52 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| I | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| M | ARG89-GLY111 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| I | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84244","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-methylated lysine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI20 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI24 |
| Number of Residues | 8 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI26 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
