8WG5
Cryo-EM structure of USP16 bound to H2AK119Ub 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 |
M | 0000278 | biological_process | mitotic cell cycle |
M | 0003713 | molecular_function | transcription coactivator activity |
M | 0004197 | molecular_function | cysteine-type endopeptidase activity |
M | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
M | 0005634 | cellular_component | nucleus |
M | 0005654 | cellular_component | nucleoplasm |
M | 0005737 | cellular_component | cytoplasm |
M | 0006325 | biological_process | chromatin organization |
M | 0006338 | biological_process | chromatin remodeling |
M | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
M | 0006508 | biological_process | proteolysis |
M | 0006974 | biological_process | DNA damage response |
M | 0008233 | molecular_function | peptidase activity |
M | 0008234 | molecular_function | cysteine-type peptidase activity |
M | 0008270 | molecular_function | zinc ion binding |
M | 0010468 | biological_process | regulation of gene expression |
M | 0016579 | biological_process | protein deubiquitination |
M | 0035520 | biological_process | monoubiquitinated protein deubiquitination |
M | 0042393 | molecular_function | histone binding |
M | 0043024 | molecular_function | ribosomal small subunit binding |
M | 0043130 | molecular_function | ubiquitin binding |
M | 0045893 | biological_process | positive regulation of DNA-templated transcription |
M | 0045901 | biological_process | positive regulation of translational elongation |
M | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
M | 0046872 | molecular_function | metal ion binding |
M | 0051289 | biological_process | protein homotetramerization |
M | 0051301 | biological_process | cell division |
M | 0051726 | biological_process | regulation of cell cycle |
M | 0090070 | biological_process | positive regulation of ribosome biogenesis |
M | 0140014 | biological_process | mitotic nuclear division |
M | 0140950 | molecular_function | histone H2A deubiquitinase activity |
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 | PS00299 |
Number of Residues | 26 |
Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
Chain | Residue | Details |
U | 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 |
site_id | PS00972 |
Number of Residues | 16 |
Details | USP_1 Ubiquitin specific protease (USP) domain signature 1. GLsnlGNtCFFNAvMQ |
Chain | Residue | Details |
M | GLY197-GLN212 |
site_id | PS00973 |
Number of Residues | 18 |
Details | USP_2 Ubiquitin specific protease (USP) domain signature 2. YsLyGVveHsGtmrs..GHY |
Chain | Residue | Details |
M | TYR742-TYR759 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 6 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435 |
Chain | Residue | Details |
D | LYS34 | |
D | LYS116 | |
D | LYS120 | |
H | LYS34 | |
H | LYS116 | |
H | LYS120 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475 |
Chain | Residue | Details |
D | GLU35 | |
H | GLU35 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q8CGP1 |
Chain | Residue | Details |
D | SER36 | |
H | SER36 | |
G | LYS74 | |
G | LYS75 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732 |
Chain | Residue | Details |
D | LYS43 | |
M | HIS103 | |
M | CYS116 | |
M | CYS119 | |
D | LYS85 | |
H | LYS43 | |
H | LYS85 | |
M | CYS74 | |
M | CYS77 | |
M | CYS82 | |
M | HIS90 | |
M | HIS94 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869 |
Chain | Residue | Details |
D | LYS46 | |
D | LYS108 | |
H | LYS46 | |
H | LYS108 |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537 |
Chain | Residue | Details |
D | LYS57 | |
H | LYS57 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08 |
Chain | Residue | Details |
D | ARG79 | |
H | ARG79 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08 |
Chain | Residue | Details |
D | ARG86 | |
D | ARG92 | |
H | ARG86 | |
H | ARG92 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729 |
Chain | Residue | Details |
D | THR115 | |
H | THR115 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
Chain | Residue | Details |
D | SER112 | |
H | SER112 | |
F | LYS91 |
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 | LYS59 | |
F | LYS79 |
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 |
D | LYS120 | |
H | LYS120 |