4R8P
Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle
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 | 0031507 | biological_process | heterochromatin formation |
| 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 | 0031507 | biological_process | heterochromatin formation |
| 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 |
| L | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| L | 0000151 | cellular_component | ubiquitin ligase complex |
| L | 0000166 | molecular_function | nucleotide binding |
| L | 0000209 | biological_process | protein polyubiquitination |
| L | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| L | 0005515 | molecular_function | protein binding |
| L | 0005524 | molecular_function | ATP binding |
| L | 0005634 | cellular_component | nucleus |
| L | 0005654 | cellular_component | nucleoplasm |
| L | 0005768 | cellular_component | endosome |
| L | 0005829 | cellular_component | cytosol |
| L | 0005886 | cellular_component | plasma membrane |
| L | 0006281 | biological_process | DNA repair |
| L | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| L | 0006513 | biological_process | protein monoubiquitination |
| L | 0006915 | biological_process | apoptotic process |
| L | 0006974 | biological_process | DNA damage response |
| L | 0010008 | cellular_component | endosome membrane |
| L | 0016020 | cellular_component | membrane |
| L | 0016567 | biological_process | protein ubiquitination |
| L | 0016740 | molecular_function | transferase activity |
| L | 0030514 | biological_process | negative regulation of BMP signaling pathway |
| L | 0036211 | biological_process | protein modification process |
| L | 0043161 | biological_process | proteasome-mediated ubiquitin-dependent protein catabolic process |
| L | 0051865 | biological_process | protein autoubiquitination |
| L | 0061630 | molecular_function | ubiquitin protein ligase activity |
| L | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| L | 0070062 | cellular_component | extracellular exosome |
| L | 0070936 | biological_process | protein K48-linked ubiquitination |
| L | 0070979 | biological_process | protein K11-linked ubiquitination |
| L | 0085020 | biological_process | protein K6-linked ubiquitination |
| L | 1903955 | biological_process | positive regulation of protein targeting to mitochondrion |
| N | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| N | 0000151 | cellular_component | ubiquitin ligase complex |
| N | 0000166 | molecular_function | nucleotide binding |
| N | 0000209 | biological_process | protein polyubiquitination |
| N | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| N | 0005515 | molecular_function | protein binding |
| N | 0005524 | molecular_function | ATP binding |
| N | 0005634 | cellular_component | nucleus |
| N | 0005654 | cellular_component | nucleoplasm |
| N | 0005768 | cellular_component | endosome |
| N | 0005829 | cellular_component | cytosol |
| N | 0005886 | cellular_component | plasma membrane |
| N | 0006281 | biological_process | DNA repair |
| N | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| N | 0006513 | biological_process | protein monoubiquitination |
| N | 0006915 | biological_process | apoptotic process |
| N | 0006974 | biological_process | DNA damage response |
| N | 0010008 | cellular_component | endosome membrane |
| N | 0016020 | cellular_component | membrane |
| N | 0016567 | biological_process | protein ubiquitination |
| N | 0016740 | molecular_function | transferase activity |
| N | 0030514 | biological_process | negative regulation of BMP signaling pathway |
| N | 0036211 | biological_process | protein modification process |
| N | 0043161 | biological_process | proteasome-mediated ubiquitin-dependent protein catabolic process |
| N | 0051865 | biological_process | protein autoubiquitination |
| N | 0061630 | molecular_function | ubiquitin protein ligase activity |
| N | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| N | 0070062 | cellular_component | extracellular exosome |
| N | 0070936 | biological_process | protein K48-linked ubiquitination |
| N | 0070979 | biological_process | protein K11-linked ubiquitination |
| N | 0085020 | biological_process | protein K6-linked ubiquitination |
| N | 1903955 | biological_process | positive regulation of protein targeting to mitochondrion |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN K 201 |
| Chain | Residue |
| K | CYS18 |
| K | CYS21 |
| K | CYS39 |
| K | CYS42 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN K 202 |
| Chain | Residue |
| K | CYS34 |
| K | HIS36 |
| K | CYS53 |
| K | CYS56 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN L 401 |
| Chain | Residue |
| L | CYS54 |
| L | CYS72 |
| L | CYS75 |
| L | CYS51 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN L 402 |
| Chain | Residue |
| L | CYS67 |
| L | HIS69 |
| L | CYS87 |
| L | THR89 |
| L | CYS90 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN M 201 |
| Chain | Residue |
| M | CYS18 |
| M | CYS21 |
| M | CYS39 |
| M | CYS42 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN M 202 |
| Chain | Residue |
| M | CYS34 |
| M | HIS36 |
| M | CYS53 |
| M | CYS56 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN N 401 |
| Chain | Residue |
| N | CYS51 |
| N | CYS54 |
| N | CYS72 |
| N | CYS75 |
| N | ARG121 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN N 402 |
| Chain | Residue |
| N | CYS67 |
| N | HIS69 |
| N | CYS87 |
| N | THR89 |
| N | CYS90 |
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 | PS00183 |
| Number of Residues | 16 |
| Details | UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL |
| Chain | Residue | Details |
| L | TYR274-LEU289 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG92-GLY114 |
| site_id | PS00518 |
| Number of Residues | 10 |
| Details | ZF_RING_1 Zinc finger RING-type signature. ClHrFCadCI |
| Chain | Residue | Details |
| L | CYS67-ILE76 | |
| K | CYS34-ILE43 |
| 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 | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250 |
| Chain | Residue | Details |
| C | SER1 | |
| G | SER1 | |
| D | LYS15 | |
| D | LYS20 | |
| H | LYS5 | |
| H | LYS12 | |
| H | LYS15 | |
| H | LYS20 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250 |
| Chain | Residue | Details |
| C | LYS5 | |
| G | LYS5 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| C | LYS9 | |
| C | LYS95 | |
| G | LYS9 | |
| G | 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 |
| C | LYS36 | |
| G | LYS36 | |
| N | LYS112 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| C | LYS74 | |
| C | LYS75 | |
| G | LYS74 | |
| G | LYS75 | |
| F | LYS8 | |
| F | LYS16 | |
| F | LYS44 | |
| F | LYS79 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: N5-methylglutamine => ECO:0000250 |
| Chain | Residue | Details |
| C | GLN104 | |
| G | GLN104 | |
| F | LYS12 | |
| F | LYS20 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P0C0S8 |
| Chain | Residue | Details |
| C | LYS118 | |
| G | LYS118 | |
| F | LYS31 | |
| F | 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 |
| C | LYS13 | |
| F | SER47 | |
| C | LYS15 | |
| C | LYS119 | |
| G | LYS13 | |
| G | LYS15 | |
| G | LYS119 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | TYR51 | |
| B | TYR88 | |
| F | TYR51 | |
| F | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| B | LYS59 | |
| E | LYS64 | |
| F | LYS59 | |
| A | LYS27 | |
| A | LYS36 | |
| A | LYS64 | |
| E | LYS18 | |
| 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 |
