8GRM
Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0003677 | molecular_function | DNA binding |
| 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 | 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 | 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 | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0003677 | molecular_function | DNA binding |
| 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 | 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 | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| N | 0000151 | cellular_component | ubiquitin ligase complex |
| P | 0000151 | cellular_component | ubiquitin ligase complex |
| P | 0000209 | biological_process | protein polyubiquitination |
| P | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| P | 0005515 | molecular_function | protein binding |
| P | 0005524 | molecular_function | ATP binding |
| P | 0005634 | cellular_component | nucleus |
| P | 0005654 | cellular_component | nucleoplasm |
| P | 0005829 | cellular_component | cytosol |
| P | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| P | 0016567 | biological_process | protein ubiquitination |
| P | 0016740 | molecular_function | transferase activity |
| P | 0019787 | molecular_function | ubiquitin-like protein transferase activity |
| P | 0031625 | molecular_function | ubiquitin protein ligase binding |
| P | 0032991 | cellular_component | protein-containing complex |
| P | 0036211 | biological_process | protein modification process |
| P | 0051865 | biological_process | protein autoubiquitination |
| P | 0061630 | molecular_function | ubiquitin protein ligase activity |
| P | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| P | 0070062 | cellular_component | extracellular exosome |
| P | 0070936 | biological_process | protein K48-linked ubiquitination |
Functional Information from PROSITE/UniProt
| site_id | PS00183 |
| Number of Residues | 16 |
| Details | UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL |
| Chain | Residue | Details |
| P | TYR74-LEU89 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| H | ARG92-GLY114 | |
| D | ARG92-GLY114 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO66-ILE74 |
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| O | LYS27-ASP52 |
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA21-VAL27 |
| site_id | PS00518 |
| Number of Residues | 10 |
| Details | ZF_RING_1 Zinc finger RING-type signature. ClHsFCktCI |
| Chain | Residue | Details |
| M | CYS34-ILE43 | |
| N | CYS67-LEU76 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: Glycyl thioester intermediate => ECO:0000255|PROSITE-ProRule:PRU00388, ECO:0000255|PROSITE-ProRule:PRU10133 |
| Chain | Residue | Details |
| H | LYS120 | |
| P | CYS85 | |
| F | LYS20 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435 |
| Chain | Residue | Details |
| B | LYS91 | |
| F | LYS31 | |
| F | LYS77 | |
| F | LYS91 | |
| B | LYS77 | |
| B | LYS31 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-propionyllysine; alternate => ECO:0000269|PubMed:17267393 |
| Chain | Residue | Details |
| G | LYS74 | |
| G | LYS75 | |
| B | LYS44 | |
| F | LYS44 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by PAK2 => ECO:0000269|PubMed:21724829, ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| F | SER47 | |
| B | SER47 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455, ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| B | TYR51 | |
| F | TYR51 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297 |
| Chain | Residue | Details |
| G | LYS118 | |
| G | LYS119 | |
| F | LYS59 | |
| B | LYS59 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62806 |
| Chain | Residue | Details |
| B | LYS79 | |
| F | LYS79 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P62806 |
| Chain | Residue | Details |
| G | LYS119 | |
| B | THR80 | |
| F | THR80 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| B | TYR88 | |
| F | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS59 | |
| B | LYS79 | |
| F | LYS20 | |
| F | LYS59 | |
| F | LYS79 | |
| B | LYS20 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:19818714 |
| Chain | Residue | Details |
| B | LYS91 | |
| F | LYS91 | |
| A | LYS122 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000269|PubMed:30886146 |
| Chain | Residue | Details |
| B | LYS31 | |
| F | LYS31 |
