6T9L
SAGA DUB module bound to a ubiqitinated nucleosome
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 | 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 | 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 |
| K | 0000124 | cellular_component | SAGA complex |
| K | 0004843 | molecular_function | cysteine-type deubiquitinase activity |
| K | 0005515 | molecular_function | protein binding |
| K | 0005634 | cellular_component | nucleus |
| K | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| K | 0006508 | biological_process | proteolysis |
| K | 0008234 | molecular_function | cysteine-type peptidase activity |
| K | 0008270 | molecular_function | zinc ion binding |
| K | 0008380 | biological_process | RNA splicing |
| K | 0016579 | biological_process | protein deubiquitination |
| K | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| K | 0046872 | molecular_function | metal ion binding |
| K | 0060090 | molecular_function | molecular adaptor activity |
| K | 0071819 | cellular_component | DUBm complex |
| L | 0000124 | cellular_component | SAGA complex |
| L | 0000932 | cellular_component | P-body |
| L | 0000973 | biological_process | post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery |
| L | 0003682 | molecular_function | chromatin binding |
| L | 0003713 | molecular_function | transcription coactivator activity |
| L | 0005515 | molecular_function | protein binding |
| L | 0005634 | cellular_component | nucleus |
| L | 0005643 | cellular_component | nuclear pore |
| L | 0005654 | cellular_component | nucleoplasm |
| L | 0005737 | cellular_component | cytoplasm |
| L | 0006325 | biological_process | chromatin organization |
| L | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| L | 0006368 | biological_process | transcription elongation by RNA polymerase II |
| L | 0006406 | biological_process | mRNA export from nucleus |
| L | 0008047 | molecular_function | enzyme activator activity |
| L | 0015031 | biological_process | protein transport |
| L | 0016973 | biological_process | poly(A)+ mRNA export from nucleus |
| L | 0032880 | biological_process | regulation of protein localization |
| L | 0043229 | cellular_component | intracellular organelle |
| L | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| L | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| L | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| L | 0051028 | biological_process | mRNA transport |
| L | 0070390 | cellular_component | transcription export complex 2 |
| L | 0071028 | biological_process | nuclear mRNA surveillance |
| L | 0071819 | cellular_component | DUBm complex |
| M | 0000124 | cellular_component | SAGA complex |
| M | 0003713 | molecular_function | transcription coactivator activity |
| M | 0005515 | molecular_function | protein binding |
| M | 0005634 | cellular_component | nucleus |
| M | 0006325 | biological_process | chromatin organization |
| M | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| M | 0008047 | molecular_function | enzyme activator activity |
| M | 0008270 | molecular_function | zinc ion binding |
| M | 0045893 | biological_process | positive regulation of DNA-templated transcription |
| M | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| M | 0046872 | molecular_function | metal ion binding |
| M | 0070461 | cellular_component | SAGA-type complex |
| M | 0071819 | cellular_component | DUBm complex |
| N | 0000124 | cellular_component | SAGA complex |
| N | 0004402 | molecular_function | histone acetyltransferase activity |
| N | 0005198 | molecular_function | structural molecule activity |
| N | 0005515 | molecular_function | protein binding |
| N | 0005634 | cellular_component | nucleus |
| N | 0005829 | cellular_component | cytosol |
| N | 0006325 | biological_process | chromatin organization |
| N | 0006338 | biological_process | chromatin remodeling |
| N | 0006357 | biological_process | regulation of transcription by RNA polymerase II |
| N | 0006406 | biological_process | mRNA export from nucleus |
| N | 0008047 | molecular_function | enzyme activator activity |
| N | 0008270 | molecular_function | zinc ion binding |
| N | 0045899 | biological_process | positive regulation of RNA polymerase II transcription preinitiation complex assembly |
| N | 0046695 | cellular_component | SLIK (SAGA-like) complex |
| N | 0046822 | biological_process | regulation of nucleocytoplasmic transport |
| N | 0065003 | biological_process | protein-containing complex assembly |
| N | 0071819 | cellular_component | DUBm complex |
| N | 1904802 | biological_process | RITS complex assembly |
| N | 1905634 | biological_process | regulation of protein localization to chromatin |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 501 |
| Chain | Residue |
| K | CYS46 |
| K | CYS49 |
| K | CYS68 |
| K | HIS73 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 502 |
| Chain | Residue |
| K | CYS60 |
| K | CYS63 |
| K | HIS77 |
| K | HIS83 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 503 |
| Chain | Residue |
| K | CYS96 |
| K | LYS98 |
| K | CYS99 |
| K | HIS6 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 504 |
| Chain | Residue |
| K | HIS170 |
| K | CYS174 |
| K | CYS182 |
| K | CYS185 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue ZN K 505 |
| Chain | Residue |
| K | HIS250 |
| K | CYS271 |
| K | CYS273 |
| K | HIS276 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue ZN K 506 |
| Chain | Residue |
| K | GLY291 |
| K | CYS292 |
| K | CYS336 |
| K | GLU338 |
| K | CYS339 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | binding site for residue ZN M 101 |
| Chain | Residue |
| M | CYS73 |
| M | ASN75 |
| M | CYS76 |
| M | HIS88 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ZN N 701 |
| Chain | Residue |
| N | CYS78 |
| N | CYS81 |
| N | HIS93 |
| N | CYS98 |
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 | PS00299 |
| Number of Residues | 26 |
| Details | UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD |
| Chain | Residue | Details |
| O | LYS27-ASP52 |
| 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 | ARG89-GLY111 | |
| H | ARG89-GLY111 |
| 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. GLinmGStCFMSSiLQ |
| Chain | Residue | Details |
| K | GLY138-GLN153 |
| site_id | PS00973 |
| Number of Residues | 18 |
| Details | USP_2 Ubiquitin specific protease (USP) domain signature 2. YeLiGIvsHkGtvne..GHY |
| Chain | Residue | Details |
| K | TYR411-TYR428 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P0C1H4 |
| Chain | Residue | Details |
| H | LYS2 | |
| H | LYS9 | |
| H | LYS12 | |
| H | LYS17 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:12757711 |
| Chain | Residue | Details |
| H | SER11 | |
| G | LYS5 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 1 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
| Chain | Residue | Details |
| H | SER109 | |
| C | LYS95 | |
| G | LYS9 | |
| G | LYS95 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250|UniProtKB:P0C1H4 |
| Chain | Residue | Details |
| H | LYS117 | |
| G | LYS36 | |
| K | CYS60 | |
| K | CYS63 | |
| K | CYS68 | |
| K | HIS73 | |
| K | HIS77 | |
| K | HIS83 |
| 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 | |
| O | LYS48 | |
| C | LYS15 | |
| C | LYS119 | |
| G | LYS13 | |
| G | LYS15 | |
| G | LYS119 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860 |
| Chain | Residue | Details |
| O | LYS27 | |
| B | TYR88 | |
| F | TYR51 | |
| F | TYR88 |
| 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:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127 |
| Chain | Residue | Details |
| O | LYS29 | |
| 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 | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577 |
| Chain | Residue | Details |
| O | LYS33 | |
| F | LYS77 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106 |
| Chain | Residue | Details |
| O | LYS63 | |
| 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 |
