6PA7
The cryo-EM structure of the human DNMT3A2-DNMT3B3 complex bound to nucleosome.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005694 | cellular_component | chromosome |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0000786 | cellular_component | nucleosome |
| D | 0003677 | molecular_function | DNA binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005694 | cellular_component | chromosome |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005694 | cellular_component | chromosome |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005634 | cellular_component | nucleus |
| F | 0005694 | cellular_component | chromosome |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0000786 | cellular_component | nucleosome |
| H | 0003677 | molecular_function | DNA binding |
| H | 0005515 | molecular_function | protein binding |
| H | 0005634 | cellular_component | nucleus |
| H | 0005694 | cellular_component | chromosome |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| K | 0006306 | biological_process | obsolete DNA methylation |
| K | 0008168 | molecular_function | methyltransferase activity |
| K | 0010468 | biological_process | regulation of gene expression |
| N | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| N | 0003677 | molecular_function | DNA binding |
| N | 0003714 | molecular_function | transcription corepressor activity |
| N | 0003886 | molecular_function | DNA (cytosine-5-)-methyltransferase activity |
| N | 0005515 | molecular_function | protein binding |
| N | 0005634 | cellular_component | nucleus |
| N | 0005654 | cellular_component | nucleoplasm |
| N | 0006306 | biological_process | obsolete DNA methylation |
| N | 0008168 | molecular_function | methyltransferase activity |
| N | 0009008 | molecular_function | DNA-methyltransferase activity |
| N | 0010468 | biological_process | regulation of gene expression |
| N | 0010605 | biological_process | negative regulation of macromolecule metabolic process |
| N | 0010628 | biological_process | positive regulation of gene expression |
| N | 0016740 | molecular_function | transferase activity |
| N | 0032259 | biological_process | methylation |
| N | 0032776 | biological_process | obsolete DNA methylation on cytosine |
| N | 0046872 | molecular_function | metal ion binding |
| N | 0051718 | molecular_function | DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates |
| N | 1902494 | cellular_component | catalytic complex |
| P | 0006306 | biological_process | obsolete DNA methylation |
| P | 0008168 | molecular_function | methyltransferase activity |
| P | 0010468 | biological_process | regulation of gene expression |
| S | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| S | 0003677 | molecular_function | DNA binding |
| S | 0003714 | molecular_function | transcription corepressor activity |
| S | 0003886 | molecular_function | DNA (cytosine-5-)-methyltransferase activity |
| S | 0005515 | molecular_function | protein binding |
| S | 0005634 | cellular_component | nucleus |
| S | 0005654 | cellular_component | nucleoplasm |
| S | 0006306 | biological_process | obsolete DNA methylation |
| S | 0008168 | molecular_function | methyltransferase activity |
| S | 0009008 | molecular_function | DNA-methyltransferase activity |
| S | 0010468 | biological_process | regulation of gene expression |
| S | 0010605 | biological_process | negative regulation of macromolecule metabolic process |
| S | 0010628 | biological_process | positive regulation of gene expression |
| S | 0016740 | molecular_function | transferase activity |
| S | 0032259 | biological_process | methylation |
| S | 0032776 | biological_process | obsolete DNA methylation on cytosine |
| S | 0046872 | molecular_function | metal ion binding |
| S | 0051718 | molecular_function | DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates |
| S | 1902494 | cellular_component | catalytic complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 2 |
| Details | binding site for residue CL A 201 |
| Chain | Residue |
| A | PRO121 |
| A | LYS122 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue CL C 201 |
| Chain | Residue |
| C | GLY46 |
| D | THR87 |
| D | SER88 |
| I | DT122 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue CL H 201 |
| Chain | Residue |
| G | GLY46 |
| H | THR87 |
| H | SER88 |
| site_id | AC4 |
| Number of Residues | 14 |
| Details | binding site for residue SAH K 1001 |
| Chain | Residue |
| K | PHE640 |
| K | ASP641 |
| K | SER663 |
| K | GLU664 |
| K | VAL665 |
| K | CYS666 |
| K | ASP686 |
| K | VAL687 |
| K | GLY707 |
| K | LEU730 |
| K | GLU756 |
| K | ARG891 |
| K | SER892 |
| K | TRP893 |
| site_id | AC5 |
| Number of Residues | 14 |
| Details | binding site for residue SAH P 1001 |
| Chain | Residue |
| P | PHE640 |
| P | ASP641 |
| P | SER663 |
| P | GLU664 |
| P | VAL665 |
| P | CYS666 |
| P | ASP686 |
| P | VAL687 |
| P | GLY707 |
| P | LEU730 |
| P | GLU756 |
| P | ARG891 |
| P | SER892 |
| P | TRP893 |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA21-VAL27 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG89-GLY111 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| B | GLY14-HIS18 |
| site_id | PS00094 |
| Number of Residues | 13 |
| Details | C5_MTASE_1 C-5 cytosine-specific DNA methylases active site. DlVigGsPCnDLS |
| Chain | Residue | Details |
| N | ASP623-SER635 | |
| K | ASP702-SER714 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS14-LEU20 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 60 |
| Details | ZN_FING: GATA-type; atypical => ECO:0000255|PROSITE-ProRule:PRU00865 |
| Chain | Residue | Details |
| N | LEU434-GLY464 | |
| S | LEU434-GLY464 | |
| D | LYS12 | |
| D | LYS17 | |
| H | LYS2 | |
| H | LYS9 | |
| H | LYS12 | |
| H | LYS17 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 112 |
| Details | ZN_FING: PHD-type; atypical => ECO:0000255|PROSITE-ProRule:PRU00865 |
| Chain | Residue | Details |
| N | CYS475-THR531 | |
| S | CYS475-THR531 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | ACT_SITE: ACT_SITE => ECO:0000255|PROSITE-ProRule:PRU01016, ECO:0000255|PROSITE-ProRule:PRU10018 |
| Chain | Residue | Details |
| N | LEU651 | |
| S | LEU651 | |
| G | LYS9 | |
| G | LYS95 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000250|UniProtKB:Q9Y6K1 |
| Chain | Residue | Details |
| N | VAL582 | |
| N | VAL605 | |
| N | GLY627 | |
| S | VAL582 | |
| S | VAL605 | |
| S | GLY627 | |
| P | ASP686 | |
| P | ARG891 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 10 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| N | SER82 | |
| S | SER202 | |
| N | SER100 | |
| N | SER110 | |
| N | SER195 | |
| N | SER202 | |
| S | SER82 | |
| S | SER100 | |
| S | SER110 | |
| S | SER195 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:21406692 |
| Chain | Residue | Details |
| N | THR96 | |
| S | THR96 | |
| P | SER255 | |
| P | SER267 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| N | SER136 | |
| S | SER136 | |
| F | LYS31 | |
| F | LYS91 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| N | SER209 | |
| S | SER209 | |
| P | SER390 | |
| P | SER393 | |
| G | LYS13 | |
| G | LYS15 | |
| G | LYS119 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline => ECO:0000250 |
| Chain | Residue | Details |
| N | SER410 | |
| S | SER410 | |
| F | TYR51 | |
| F | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| N | LYS89 | |
| E | LYS64 | |
| F | LYS59 | |
| N | GLU617 | |
| S | LYS89 | |
| A | LYS64 | |
| S | GLU617 | |
| E | LYS23 | |
| E | LYS27 | |
| E | LYS36 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS77 | |
| F | 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 |
| B | LYS31 | |
| F | 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 |
| A | LYS37 | |
| B | LYS91 | |
| F | LYS91 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | TYR41 | |
| E | TYR41 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| A | LYS56 | |
| A | LYS79 | |
| E | LYS56 | |
| E | LYS79 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | SER57 | |
| E | SER57 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | THR80 | |
| A | THR107 | |
| E | THR80 | |
| E | THR107 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER86 | |
| E | SER86 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS115 | |
| E | LYS115 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS122 | |
| E | LYS122 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | CYS110 | |
| E | CYS110 |
