9Y4P
Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| a | 0008168 | molecular_function | methyltransferase activity |
| a | 0010468 | biological_process | regulation of gene expression |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005694 | cellular_component | chromosome |
| A | 0006334 | biological_process | nucleosome assembly |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| b | 0008168 | molecular_function | methyltransferase activity |
| b | 0009008 | molecular_function | DNA-methyltransferase activity |
| b | 0010468 | biological_process | regulation of gene expression |
| 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 | 0031507 | biological_process | heterochromatin formation |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| c | 0008168 | molecular_function | methyltransferase activity |
| c | 0010468 | biological_process | regulation of gene expression |
| 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 | 0031507 | biological_process | heterochromatin formation |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| d | 0008168 | molecular_function | methyltransferase activity |
| d | 0010468 | biological_process | regulation of gene expression |
| D | 0000786 | cellular_component | nucleosome |
| D | 0002227 | biological_process | innate immune response in mucosa |
| D | 0003677 | molecular_function | DNA binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005576 | cellular_component | extracellular region |
| D | 0005634 | cellular_component | nucleus |
| D | 0005694 | cellular_component | chromosome |
| D | 0006325 | biological_process | chromatin organization |
| D | 0019731 | biological_process | antibacterial humoral response |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0031507 | biological_process | heterochromatin formation |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| e | 0008168 | molecular_function | methyltransferase activity |
| e | 0009008 | molecular_function | DNA-methyltransferase activity |
| e | 0010468 | biological_process | regulation of gene expression |
| 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 | 0006334 | biological_process | nucleosome assembly |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0031507 | biological_process | heterochromatin formation |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| f | 0008168 | molecular_function | methyltransferase activity |
| f | 0010468 | biological_process | regulation of gene expression |
| 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 | 0031507 | biological_process | heterochromatin formation |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| g | 0008168 | molecular_function | methyltransferase activity |
| g | 0009008 | molecular_function | DNA-methyltransferase activity |
| g | 0010468 | biological_process | regulation of gene expression |
| 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 | 0031507 | biological_process | heterochromatin formation |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0000786 | cellular_component | nucleosome |
| H | 0002227 | biological_process | innate immune response in mucosa |
| H | 0003677 | molecular_function | DNA binding |
| H | 0005515 | molecular_function | protein binding |
| H | 0005576 | cellular_component | extracellular region |
| H | 0005634 | cellular_component | nucleus |
| H | 0005694 | cellular_component | chromosome |
| H | 0006325 | biological_process | chromatin organization |
| H | 0019731 | biological_process | antibacterial humoral response |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0031507 | biological_process | heterochromatin formation |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| P | 0000786 | cellular_component | nucleosome |
| P | 0002227 | biological_process | innate immune response in mucosa |
| P | 0003677 | molecular_function | DNA binding |
| P | 0005515 | molecular_function | protein binding |
| P | 0005576 | cellular_component | extracellular region |
| P | 0005634 | cellular_component | nucleus |
| P | 0005694 | cellular_component | chromosome |
| P | 0006325 | biological_process | chromatin organization |
| P | 0019731 | biological_process | antibacterial humoral response |
| P | 0030527 | molecular_function | structural constituent of chromatin |
| P | 0031507 | biological_process | heterochromatin formation |
| P | 0046982 | molecular_function | protein heterodimerization activity |
| P | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| Q | 0000786 | cellular_component | nucleosome |
| Q | 0003677 | molecular_function | DNA binding |
| Q | 0005515 | molecular_function | protein binding |
| Q | 0005634 | cellular_component | nucleus |
| Q | 0005654 | cellular_component | nucleoplasm |
| 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 | 0005515 | molecular_function | protein binding |
| R | 0005634 | cellular_component | nucleus |
| R | 0005694 | cellular_component | chromosome |
| R | 0006334 | biological_process | nucleosome assembly |
| 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 | 0005634 | cellular_component | nucleus |
| S | 0005694 | cellular_component | chromosome |
| S | 0030527 | molecular_function | structural constituent of chromatin |
| S | 0031507 | biological_process | heterochromatin formation |
| S | 0046982 | molecular_function | protein heterodimerization activity |
| T | 0000786 | cellular_component | nucleosome |
| T | 0002227 | biological_process | innate immune response in mucosa |
| T | 0003677 | molecular_function | DNA binding |
| T | 0005515 | molecular_function | protein binding |
| T | 0005576 | cellular_component | extracellular region |
| T | 0005634 | cellular_component | nucleus |
| T | 0005694 | cellular_component | chromosome |
| T | 0006325 | biological_process | chromatin organization |
| T | 0019731 | biological_process | antibacterial humoral response |
| T | 0030527 | molecular_function | structural constituent of chromatin |
| T | 0031507 | biological_process | heterochromatin formation |
| T | 0046982 | molecular_function | protein heterodimerization activity |
| T | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| W | 0000786 | cellular_component | nucleosome |
| W | 0003677 | molecular_function | DNA binding |
| W | 0005515 | molecular_function | protein binding |
| W | 0005634 | cellular_component | nucleus |
| W | 0005654 | cellular_component | nucleoplasm |
| W | 0005694 | cellular_component | chromosome |
| W | 0006334 | biological_process | nucleosome assembly |
| W | 0030527 | molecular_function | structural constituent of chromatin |
| W | 0031507 | biological_process | heterochromatin formation |
| W | 0046982 | molecular_function | protein heterodimerization activity |
| X | 0000786 | cellular_component | nucleosome |
| X | 0003677 | molecular_function | DNA binding |
| X | 0005515 | molecular_function | protein binding |
| X | 0005634 | cellular_component | nucleus |
| X | 0005694 | cellular_component | chromosome |
| X | 0006334 | biological_process | nucleosome assembly |
| X | 0030527 | molecular_function | structural constituent of chromatin |
| X | 0031507 | biological_process | heterochromatin formation |
| X | 0046982 | molecular_function | protein heterodimerization activity |
| Y | 0000786 | cellular_component | nucleosome |
| Y | 0003677 | molecular_function | DNA binding |
| Y | 0005634 | cellular_component | nucleus |
| Y | 0005694 | cellular_component | chromosome |
| Y | 0030527 | molecular_function | structural constituent of chromatin |
| Y | 0031507 | biological_process | heterochromatin formation |
| Y | 0046982 | molecular_function | protein heterodimerization activity |
| Z | 0008168 | molecular_function | methyltransferase activity |
| Z | 0009008 | molecular_function | DNA-methyltransferase activity |
| Z | 0010468 | biological_process | regulation of gene expression |
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 | 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 |
| b | ASP623-SER635 | |
| a | ASP702-SER714 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS14-LEU20 | |
| E | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG89-GLY111 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO66-ILE74 | |
| E | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| 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_FI10 |
| Number of Residues | 8 |
| 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_FI11 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-isonicotinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-benzoyllysine; alternate","evidences":[{"source":"UniProtKB","id":"C0HKE1","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| 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_FI17 |
| Number of Residues | 8 |
| Details | Modified residue: {"description":"N6-isonicotinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q93079","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 12 |
| Details | Modified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q93079","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI20 |
| Number of Residues | 8 |
| 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 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI22 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI23 |
| Number of Residues | 6 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI24 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI25 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI26 |
| Number of Residues | 6 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI27 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI28 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI29 |
| Number of Residues | 3 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI30 |
| Number of Residues | 3 |
| Details | Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI31 |
| Number of Residues | 660 |
| Details | Domain: {"description":"ADD","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI32 |
| Number of Residues | 180 |
| Details | Zinc finger: {"description":"GATA-type; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI33 |
| Number of Residues | 280 |
| Details | Zinc finger: {"description":"PHD-type; atypical","evidences":[{"source":"PROSITE-ProRule","id":"PRU00865","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI34 |
| Number of Residues | 184 |
| Details | Region: {"description":"Interaction with the PRC2/EED-EZH2 complex","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI35 |
| Number of Residues | 7 |
| Details | Active site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU01016","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10018","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI36 |
| Number of Residues | 30 |
| Details | Binding site: {"evidences":[{"source":"UniProtKB","id":"Q9Y6K1","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI37 |
| Number of Residues | 8 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI38 |
| Number of Residues | 116 |
| Details | Domain: {"description":"PWWP","evidences":[{"source":"PROSITE-ProRule","id":"PRU00162","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI39 |
| Number of Residues | 276 |
| Details | Region: {"description":"Interaction with the PRC2/EED-EZH2 complex","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI40 |
| Number of Residues | 36 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"17713477","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2QRV","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI41 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"S-methylcysteine; by autocatalysis","evidences":[{"source":"UniProtKB","id":"O88508","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
