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 | 0031492 | molecular_function | nucleosomal DNA binding |
| A | 0031507 | biological_process | heterochromatin formation |
| 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 | 0031507 | biological_process | heterochromatin formation |
| 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 | 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 | 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 | 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 | 0031492 | molecular_function | nucleosomal DNA binding |
| E | 0031507 | biological_process | heterochromatin formation |
| 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 | 0031507 | biological_process | heterochromatin formation |
| 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 | 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 | 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 |
| 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 | 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 | 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 | 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 | 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 | 1 |
| Details | Modified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| 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_FI19 |
| Number of Residues | 4 |
| 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_FI20 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI21 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI25 |
| Number of Residues | 5 |
| 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_FI26 |
| Number of Residues | 2 |
| Details | Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI27 |
| Number of Residues | 4 |
| 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_FI28 |
| Number of Residues | 158 |
| Details | Zinc finger: {"description":"RING-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00175","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI29 |
| Number of Residues | 28 |
| Details | Motif: {"description":"Nuclear localization signal","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI30 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI31 |
| Number of Residues | 10 |
| Details | Region: {"description":"Interaction with nucleosomes via an acidic patch on histone H2A and histone H2B","evidences":[{"source":"PubMed","id":"25355358","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI32 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"25519132","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI33 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"Q9CQJ4","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
