8U5H
Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| I | 0000786 | cellular_component | nucleosome |
| I | 0003677 | molecular_function | DNA binding |
| I | 0005634 | cellular_component | nucleus |
| I | 0005694 | cellular_component | chromosome |
| I | 0030527 | molecular_function | structural constituent of chromatin |
| I | 0046982 | molecular_function | protein heterodimerization activity |
| 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 | 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 | 0003677 | molecular_function | DNA binding |
| M | 0005515 | molecular_function | protein binding |
| M | 0005634 | cellular_component | nucleus |
| M | 0005694 | cellular_component | chromosome |
| M | 0030527 | molecular_function | structural constituent of chromatin |
| M | 0046982 | molecular_function | protein heterodimerization activity |
| O | 0000786 | cellular_component | nucleosome |
| O | 0003677 | molecular_function | DNA binding |
| O | 0005634 | cellular_component | nucleus |
| O | 0005694 | cellular_component | chromosome |
| O | 0030527 | molecular_function | structural constituent of chromatin |
| O | 0046982 | molecular_function | protein heterodimerization activity |
| 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 | 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 | 0003677 | molecular_function | DNA binding |
| S | 0005515 | molecular_function | protein binding |
| S | 0005634 | cellular_component | nucleus |
| S | 0005694 | cellular_component | chromosome |
| S | 0030527 | molecular_function | structural constituent of chromatin |
| S | 0046982 | molecular_function | protein heterodimerization activity |
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 | MOD_RES: Phosphoserine => ECO:0000250 |
| Chain | Residue | Details |
| K | SER1 | |
| R | SER1 | |
| M | LYS12 | |
| M | LYS17 | |
| S | LYS2 | |
| S | LYS9 | |
| S | LYS12 | |
| S | LYS17 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250 |
| Chain | Residue | Details |
| K | LYS5 | |
| R | LYS5 | |
| B | LYS162 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| K | LYS9 | |
| K | LYS95 | |
| R | LYS9 | |
| R | LYS95 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| K | LYS36 | |
| R | LYS36 | |
| S | LYS117 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| K | LYS74 | |
| K | LYS75 | |
| R | LYS74 | |
| R | LYS75 | |
| Q | LYS8 | |
| Q | LYS16 | |
| Q | LYS44 | |
| Q | LYS79 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N5-methylglutamine => ECO:0000250 |
| Chain | Residue | Details |
| K | GLN104 | |
| R | GLN104 | |
| Q | LYS12 | |
| Q | LYS20 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| K | LYS118 | |
| R | LYS118 | |
| Q | LYS31 | |
| Q | LYS91 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250 |
| Chain | Residue | Details |
| K | LYS13 | |
| Q | SER47 | |
| K | LYS15 | |
| K | CYS119 | |
| R | LYS13 | |
| R | LYS15 | |
| R | CYS119 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| J | TYR51 | |
| J | TYR88 | |
| Q | TYR51 | |
| Q | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| J | LYS59 | |
| Q | LYS59 | |
| I | LYS36 | |
| O | LYS18 | |
| O | LYS27 | |
| O | LYS36 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| J | LYS77 | |
| Q | LYS77 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| J | LYS31 | |
| Q | LYS31 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| I | LYS56 | |
| J | LYS91 | |
| O | LYS56 | |
| Q | LYS91 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| I | SER57 | |
| O | SER57 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| I | THR80 | |
| O | THR80 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| I | LYS115 | |
| O | LYS115 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| I | LYS122 | |
| O | LYS122 |
