8X7I
Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy
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 |
| K | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| K | 0000166 | molecular_function | nucleotide binding |
| K | 0000209 | biological_process | protein polyubiquitination |
| K | 0004842 | molecular_function | ubiquitin-protein transferase activity |
| K | 0005515 | molecular_function | protein binding |
| K | 0005524 | molecular_function | ATP binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0005654 | cellular_component | nucleoplasm |
| K | 0005768 | cellular_component | endosome |
| K | 0005829 | cellular_component | cytosol |
| K | 0005886 | cellular_component | plasma membrane |
| K | 0006281 | biological_process | DNA repair |
| K | 0006511 | biological_process | ubiquitin-dependent protein catabolic process |
| K | 0006513 | biological_process | protein monoubiquitination |
| K | 0006915 | biological_process | apoptotic process |
| K | 0006974 | biological_process | DNA damage response |
| K | 0010008 | cellular_component | endosome membrane |
| K | 0016020 | cellular_component | membrane |
| K | 0016567 | biological_process | protein ubiquitination |
| K | 0016740 | molecular_function | transferase activity |
| K | 0030514 | biological_process | negative regulation of BMP signaling pathway |
| K | 0036211 | biological_process | protein modification process |
| K | 0043161 | biological_process | proteasome-mediated ubiquitin-dependent protein catabolic process |
| K | 0051865 | biological_process | protein autoubiquitination |
| K | 0061630 | molecular_function | ubiquitin protein ligase activity |
| K | 0061631 | molecular_function | ubiquitin conjugating enzyme activity |
| K | 0070062 | cellular_component | extracellular exosome |
| K | 0070936 | biological_process | protein K48-linked ubiquitination |
| K | 0070979 | biological_process | protein K11-linked ubiquitination |
| K | 0085020 | biological_process | protein K6-linked ubiquitination |
| K | 1903955 | biological_process | positive regulation of protein targeting to mitochondrion |
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 | |
| G | ALA21-VAL27 |
| site_id | PS00183 |
| Number of Residues | 16 |
| Details | UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL |
| Chain | Residue | Details |
| K | TYR74-LEU89 |
| site_id | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| M | LYS27-ASP52 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| 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 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | SITE: Interacts with activating enzyme |
| Chain | Residue | Details |
| M | ARG54 | |
| M | ARG72 | |
| D | LYS120 | |
| H | LYS34 | |
| H | LYS116 | |
| H | LYS120 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | SITE: Essential for function |
| Chain | Residue | Details |
| M | HIS68 | |
| H | GLU35 | |
| B | LYS91 | |
| F | LYS31 | |
| F | LYS77 | |
| F | LYS91 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| 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 |
| M | SER65 | |
| H | SER36 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457 |
| Chain | Residue | Details |
| M | THR66 | |
| D | LYS85 | |
| H | LYS43 | |
| H | LYS85 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603 |
| Chain | Residue | Details |
| M | LYS6 | |
| D | LYS108 | |
| H | LYS46 | |
| H | LYS108 |
| 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:16543144, ECO:0000269|PubMed:18719106 |
| Chain | Residue | Details |
| D | LYS57 | |
| M | LYS63 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144 |
| Chain | Residue | Details |
| M | LYS11 | |
| M | LYS48 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 |
| Chain | Residue | Details |
| M | LYS27 | |
| D | ARG92 | |
| H | ARG86 | |
| H | ARG92 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| 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 |
| M | LYS29 | |
| H | THR115 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 |
| Chain | Residue | Details |
| M | LYS33 | |
| H | SER112 | |
| B | LYS79 | |
| F | LYS20 | |
| F | LYS59 | |
| F | LYS79 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816 |
| Chain | Residue | Details |
| D | LYS34 | |
| H | LYS34 | |
| F | LYS91 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563 |
| Chain | Residue | Details |
| B | LYS31 | |
| D | LYS120 | |
| H | LYS120 |
