7BWD
Structure of Dot1L-H2BK34ub Nucleosome Complex
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 | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006334 | biological_process | nucleosome assembly |
| A | 0010467 | biological_process | gene expression |
| A | 0016020 | cellular_component | membrane |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0032200 | biological_process | telomere organization |
| A | 0032991 | cellular_component | protein-containing complex |
| A | 0040029 | biological_process | epigenetic regulation of gene expression |
| A | 0045296 | molecular_function | cadherin binding |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000781 | cellular_component | chromosome, telomeric region |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0016020 | cellular_component | membrane |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0032200 | biological_process | telomere organization |
| B | 0032991 | cellular_component | protein-containing complex |
| B | 0043505 | cellular_component | CENP-A containing nucleosome |
| B | 0045653 | biological_process | negative regulation of megakaryocyte differentiation |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| B | 0070062 | cellular_component | extracellular exosome |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0006325 | biological_process | chromatin organization |
| C | 0008285 | biological_process | negative regulation of cell population proliferation |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0031507 | biological_process | heterochromatin formation |
| C | 0043505 | cellular_component | CENP-A containing nucleosome |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| C | 0070062 | cellular_component | extracellular exosome |
| 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 | 0005615 | cellular_component | extracellular space |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005694 | cellular_component | chromosome |
| D | 0005829 | cellular_component | cytosol |
| D | 0019731 | biological_process | antibacterial humoral response |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0031640 | biological_process | killing of cells of another organism |
| D | 0042742 | biological_process | defense response to bacterium |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0050829 | biological_process | defense response to Gram-negative bacterium |
| D | 0050830 | biological_process | defense response to Gram-positive bacterium |
| D | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005576 | cellular_component | extracellular region |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005694 | cellular_component | chromosome |
| E | 0006325 | biological_process | chromatin organization |
| E | 0006334 | biological_process | nucleosome assembly |
| E | 0010467 | biological_process | gene expression |
| E | 0016020 | cellular_component | membrane |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0032200 | biological_process | telomere organization |
| E | 0032991 | cellular_component | protein-containing complex |
| E | 0040029 | biological_process | epigenetic regulation of gene expression |
| E | 0045296 | molecular_function | cadherin binding |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0070062 | cellular_component | extracellular exosome |
| F | 0000781 | cellular_component | chromosome, telomeric region |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0003723 | molecular_function | RNA binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005576 | cellular_component | extracellular region |
| F | 0005634 | cellular_component | nucleus |
| F | 0005654 | cellular_component | nucleoplasm |
| F | 0005694 | cellular_component | chromosome |
| F | 0006325 | biological_process | chromatin organization |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0016020 | cellular_component | membrane |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0032200 | biological_process | telomere organization |
| F | 0032991 | cellular_component | protein-containing complex |
| F | 0043505 | cellular_component | CENP-A containing nucleosome |
| F | 0045653 | biological_process | negative regulation of megakaryocyte differentiation |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| F | 0070062 | cellular_component | extracellular exosome |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005515 | molecular_function | protein binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0006325 | biological_process | chromatin organization |
| G | 0008285 | biological_process | negative regulation of cell population proliferation |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0031507 | biological_process | heterochromatin formation |
| G | 0043505 | cellular_component | CENP-A containing nucleosome |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| G | 0070062 | cellular_component | extracellular exosome |
| 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 | 0005615 | cellular_component | extracellular space |
| H | 0005634 | cellular_component | nucleus |
| H | 0005654 | cellular_component | nucleoplasm |
| H | 0005694 | cellular_component | chromosome |
| H | 0005829 | cellular_component | cytosol |
| H | 0019731 | biological_process | antibacterial humoral response |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0031640 | biological_process | killing of cells of another organism |
| H | 0042742 | biological_process | defense response to bacterium |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0050829 | biological_process | defense response to Gram-negative bacterium |
| H | 0050830 | biological_process | defense response to Gram-positive bacterium |
| H | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| K | 0031151 | molecular_function | histone H3K79 methyltransferase activity |
| K | 0051726 | biological_process | regulation of cell cycle |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 15 |
| Details | binding site for residue SAH K 501 |
| Chain | Residue |
| K | PRO133 |
| K | VAL169 |
| K | GLU186 |
| K | PHE223 |
| K | PHE239 |
| K | ASN241 |
| K | PHE245 |
| K | GLU134 |
| K | VAL135 |
| K | TYR136 |
| K | THR139 |
| K | ASP161 |
| K | GLY163 |
| K | SER164 |
| K | GLN168 |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| G | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| F | GLY14-HIS18 |
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| L | LYS27-ASP52 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| E | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| H | ARG92-GLY114 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| E | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | SITE: Interacts with activating enzyme |
| Chain | Residue | Details |
| L | ARG54 | |
| L | ARG72 | |
| M | ARG54 | |
| M | ARG72 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | SITE: Essential for function |
| Chain | Residue | Details |
| L | HIS68 | |
| M | HIS68 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291 |
| Chain | Residue | Details |
| L | SER65 | |
| D | LYS11 | |
| D | LYS15 | |
| D | LYS16 | |
| D | LYS20 | |
| D | LYS23 | |
| D | LYS43 | |
| D | LYS85 | |
| M | SER65 | |
| H | LYS15 | |
| H | LYS16 | |
| H | LYS20 | |
| H | LYS23 | |
| H | LYS43 | |
| H | LYS85 | |
| D | LYS5 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 |
| Chain | Residue | Details |
| L | THR66 | |
| M | THR66 | |
| C | LYS9 | |
| C | LYS95 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742 |
| Chain | Residue | Details |
| L | CYS76 | |
| M | CYS76 | |
| F | LYS44 | |
| B | LYS8 | |
| B | LYS16 | |
| B | LYS44 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 |
| Chain | Residue | Details |
| L | LYS6 | |
| M | LYS6 | |
| F | LYS77 | |
| F | LYS91 | |
| B | LYS12 | |
| B | LYS31 | |
| B | LYS77 | |
| B | LYS91 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins) |
| Chain | Residue | Details |
| E | LYS9 | |
| L | CYS76 | |
| C | LYS74 | |
| M | CYS76 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 |
| Chain | Residue | Details |
| L | LYS11 | |
| L | LYS48 | |
| M | LYS11 | |
| M | LYS48 | |
| D | LYS116 | |
| D | LYS120 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 |
| Chain | Residue | Details |
| L | LYS27 | |
| M | LYS27 | |
| G | LYS125 | |
| C | LYS118 | |
| C | LYS119 | |
| C | LYS125 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 |
| Chain | Residue | Details |
| L | LYS29 | |
| M | LYS29 | |
| A | LYS14 | |
| A | LYS56 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 |
| Chain | Residue | Details |
| L | LYS33 | |
| M | LYS33 | |
| D | LYS46 | |
| D | LYS108 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 |
| Chain | Residue | Details |
| L | LYS63 | |
| M | LYS63 | |
| A | LYS18 | |
| A | LYS64 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | LYS23 | |
| A | LYS23 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline => ECO:0000269|PubMed:16567635 |
| Chain | Residue | Details |
| E | ARG26 | |
| A | ARG26 | |
| D | ARG86 | |
| D | ARG92 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | LYS27 | |
| A | LYS27 | |
| B | LYS91 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:15684425, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16457588 |
| Chain | Residue | Details |
| E | SER28 | |
| A | SER28 | |
| F | LYS79 | |
| B | LYS20 | |
| B | LYS59 | |
| B | LYS79 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:15983376, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:17194708 |
| Chain | Residue | Details |
| E | LYS36 | |
| A | LYS36 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine => ECO:0000269|PubMed:15983376 |
| Chain | Residue | Details |
| E | LYS37 | |
| A | LYS37 | |
| D | LYS120 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:19783980 |
| Chain | Residue | Details |
| E | TYR41 | |
| A | TYR41 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:20850016 |
| Chain | Residue | Details |
| E | SER57 | |
| A | SER57 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711 |
| Chain | Residue | Details |
| E | LYS79 | |
| A | LYS79 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016 |
| Chain | Residue | Details |
| E | THR80 | |
| A | THR80 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| E | SER86 | |
| A | SER86 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| E | THR107 | |
| A | THR107 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297 |
| Chain | Residue | Details |
| E | LYS115 | |
| A | LYS115 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229 |
| Chain | Residue | Details |
| E | LYS122 | |
| A | LYS122 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 2 |
| Details | LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806 |
| Chain | Residue | Details |
| E | LYS18 | |
| A | LYS18 |
