5GSU
Crystal structure of nucleosome core particle consisting of human testis-specific histone variants, Th2A and Th2B
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 | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006334 | biological_process | nucleosome assembly |
| A | 0010467 | biological_process | gene expression |
| A | 0016020 | cellular_component | membrane |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0032200 | biological_process | telomere organization |
| A | 0032991 | cellular_component | protein-containing complex |
| A | 0040029 | biological_process | epigenetic regulation of gene expression |
| A | 0045296 | molecular_function | cadherin binding |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000781 | cellular_component | chromosome, telomeric region |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0016020 | cellular_component | membrane |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0032200 | biological_process | telomere organization |
| B | 0032991 | cellular_component | protein-containing complex |
| B | 0043505 | cellular_component | CENP-A containing nucleosome |
| B | 0045653 | biological_process | negative regulation of megakaryocyte differentiation |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| B | 0070062 | cellular_component | extracellular exosome |
| C | 0000781 | cellular_component | chromosome, telomeric region |
| C | 0000786 | cellular_component | nucleosome |
| C | 0001674 | cellular_component | female germ cell nucleus |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0006325 | biological_process | chromatin organization |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0031492 | molecular_function | nucleosomal DNA binding |
| C | 0031507 | biological_process | heterochromatin formation |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0070062 | cellular_component | extracellular exosome |
| D | 0000781 | cellular_component | chromosome, telomeric region |
| D | 0000786 | cellular_component | nucleosome |
| D | 0001674 | cellular_component | female germ cell nucleus |
| D | 0003674 | molecular_function | molecular_function |
| D | 0003677 | molecular_function | DNA binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005694 | cellular_component | chromosome |
| D | 0006325 | biological_process | chromatin organization |
| D | 0006334 | biological_process | nucleosome assembly |
| D | 0006337 | biological_process | nucleosome disassembly |
| D | 0006954 | biological_process | inflammatory response |
| D | 0009986 | cellular_component | cell surface |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0031639 | biological_process | plasminogen activation |
| D | 0035092 | biological_process | sperm DNA condensation |
| D | 0042393 | molecular_function | histone binding |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0051276 | biological_process | chromosome organization |
| D | 0071674 | biological_process | mononuclear cell migration |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005576 | cellular_component | extracellular region |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005694 | cellular_component | chromosome |
| E | 0006325 | biological_process | chromatin organization |
| E | 0006334 | biological_process | nucleosome assembly |
| E | 0010467 | biological_process | gene expression |
| E | 0016020 | cellular_component | membrane |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0032200 | biological_process | telomere organization |
| E | 0032991 | cellular_component | protein-containing complex |
| E | 0040029 | biological_process | epigenetic regulation of gene expression |
| E | 0045296 | molecular_function | cadherin binding |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0070062 | cellular_component | extracellular exosome |
| F | 0000781 | cellular_component | chromosome, telomeric region |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0003723 | molecular_function | RNA binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005576 | cellular_component | extracellular region |
| F | 0005634 | cellular_component | nucleus |
| F | 0005654 | cellular_component | nucleoplasm |
| F | 0005694 | cellular_component | chromosome |
| F | 0006325 | biological_process | chromatin organization |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0016020 | cellular_component | membrane |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0032200 | biological_process | telomere organization |
| F | 0032991 | cellular_component | protein-containing complex |
| F | 0043505 | cellular_component | CENP-A containing nucleosome |
| F | 0045653 | biological_process | negative regulation of megakaryocyte differentiation |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| F | 0070062 | cellular_component | extracellular exosome |
| G | 0000781 | cellular_component | chromosome, telomeric region |
| G | 0000786 | cellular_component | nucleosome |
| G | 0001674 | cellular_component | female germ cell nucleus |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0006325 | biological_process | chromatin organization |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0031492 | molecular_function | nucleosomal DNA binding |
| G | 0031507 | biological_process | heterochromatin formation |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0070062 | cellular_component | extracellular exosome |
| H | 0000781 | cellular_component | chromosome, telomeric region |
| H | 0000786 | cellular_component | nucleosome |
| H | 0001674 | cellular_component | female germ cell nucleus |
| H | 0003674 | molecular_function | molecular_function |
| H | 0003677 | molecular_function | DNA binding |
| H | 0005634 | cellular_component | nucleus |
| H | 0005654 | cellular_component | nucleoplasm |
| H | 0005694 | cellular_component | chromosome |
| H | 0006325 | biological_process | chromatin organization |
| H | 0006334 | biological_process | nucleosome assembly |
| H | 0006337 | biological_process | nucleosome disassembly |
| H | 0006954 | biological_process | inflammatory response |
| H | 0009986 | cellular_component | cell surface |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0031639 | biological_process | plasminogen activation |
| H | 0035092 | biological_process | sperm DNA condensation |
| H | 0042393 | molecular_function | histone binding |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0051276 | biological_process | chromosome organization |
| H | 0071674 | biological_process | mononuclear cell migration |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | binding site for residue CL G 201 |
| Chain | Residue |
| G | GLY46 |
| G | ALA47 |
| G | GLY48 |
| H | SER89 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | binding site for residue MN D 201 |
| Chain | Residue |
| C | GLU66 |
| D | VAL46 |
| D | MN202 |
| E | ASP77 |
| site_id | AC3 |
| Number of Residues | 4 |
| Details | binding site for residue MN D 202 |
| Chain | Residue |
| D | VAL46 |
| D | MN201 |
| E | ASP77 |
| D | GLN45 |
| site_id | AC4 |
| Number of Residues | 1 |
| Details | binding site for residue MN I 201 |
| Chain | Residue |
| I | DC84 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue MN I 203 |
| Chain | Residue |
| I | DA133 |
| I | DG134 |
| I | MN204 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | binding site for residue MN I 204 |
| Chain | Residue |
| I | DA133 |
| I | MN203 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue MN I 206 |
| Chain | Residue |
| I | DG121 |
| I | CL209 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | binding site for residue MN I 207 |
| Chain | Residue |
| I | DT136 |
| I | DG137 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue CL I 209 |
| Chain | Residue |
| I | DT120 |
| I | MN206 |
| site_id | AD1 |
| Number of Residues | 1 |
| Details | binding site for residue MN J 301 |
| Chain | Residue |
| J | DG246 |
| site_id | AD2 |
| Number of Residues | 1 |
| Details | binding site for residue MN J 302 |
| Chain | Residue |
| J | DG267 |
| site_id | AD3 |
| Number of Residues | 1 |
| Details | binding site for residue MN J 303 |
| Chain | Residue |
| J | DG217 |
| site_id | AD4 |
| Number of Residues | 1 |
| Details | binding site for residue MN J 304 |
| Chain | Residue |
| J | DG280 |
| site_id | AD5 |
| Number of Residues | 2 |
| Details | binding site for residue MN J 305 |
| Chain | Residue |
| J | DC172 |
| J | DA173 |
| site_id | AD6 |
| Number of Residues | 1 |
| Details | binding site for residue CL J 306 |
| Chain | Residue |
| J | DG268 |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA23-VAL29 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| B | GLY14-HIS18 |
| 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 | ARG90-GLY112 |
| 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: N-acetylproline => ECO:0000250|UniProtKB:P23527 |
| Chain | Residue | Details |
| D | PRO-2 | |
| H | PRO-2 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 16 |
| Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732 |
| Chain | Residue | Details |
| D | LYS3 | |
| H | LYS9 | |
| H | LYS13 | |
| H | LYS14 | |
| H | LYS18 | |
| H | LYS21 | |
| H | LYS41 | |
| H | LYS83 | |
| D | LYS9 | |
| D | LYS13 | |
| D | LYS14 | |
| D | LYS18 | |
| D | LYS21 | |
| D | LYS41 | |
| D | LYS83 | |
| H | LYS3 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322 |
| Chain | Residue | Details |
| D | LYS10 | |
| H | LYS10 | |
| C | LYS77 | |
| G | LYS7 | |
| G | LYS76 | |
| G | LYS77 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P33778 |
| Chain | Residue | Details |
| D | LYS32 | |
| D | LYS114 | |
| D | LYS118 | |
| H | LYS32 | |
| H | LYS114 | |
| H | LYS118 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q64475 |
| Chain | Residue | Details |
| D | SER34 | |
| H | SER34 | |
| B | LYS44 | |
| F | LYS8 | |
| F | LYS16 | |
| F | LYS44 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P62807 |
| Chain | Residue | Details |
| D | LYS44 | |
| D | LYS106 | |
| H | LYS44 | |
| H | LYS106 | |
| F | LYS12 | |
| F | LYS31 | |
| F | LYS77 | |
| F | LYS91 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P62807 |
| Chain | Residue | Details |
| D | LYS55 | |
| H | LYS55 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Dimethylated arginine => ECO:0000269|PubMed:21249133 |
| Chain | Residue | Details |
| D | ARG77 | |
| H | ARG77 | |
| G | LYS120 | |
| G | LYS121 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:21249133 |
| Chain | Residue | Details |
| D | SER82 | |
| H | SER82 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: Omega-N-methylarginine => ECO:0000269|PubMed:21249133 |
| Chain | Residue | Details |
| D | ARG84 | |
| D | ARG90 | |
| H | ARG84 | |
| H | ARG90 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729 |
| Chain | Residue | Details |
| D | THR113 | |
| H | THR113 | |
| G | LYS15 | |
| G | LYS17 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876 |
| Chain | Residue | Details |
| D | LYS3 | |
| H | LYS3 | |
| E | LYS18 | |
| G | LYS121 |
| site_id | SWS_FT_FI13 |
| 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:16713563 |
| Chain | Residue | Details |
| B | TYR88 | |
| D | LYS118 | |
| H | LYS118 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6 |
| Chain | Residue | Details |
| D | LYS18 | |
| H | LYS18 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250|UniProtKB:P33778 |
| Chain | Residue | Details |
| D | LYS32 | |
| H | LYS32 | |
| F | LYS91 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 6 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| B | LYS20 | |
| B | LYS59 | |
| B | LYS79 | |
| F | LYS20 | |
| F | LYS59 | |
| F | LYS79 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000269|PubMed:30886146 |
| Chain | Residue | Details |
| B | LYS31 | |
| F | LYS31 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine => ECO:0000269|PubMed:15983376 |
| Chain | Residue | Details |
| A | LYS37 | |
| E | LYS37 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:19783980 |
| Chain | Residue | Details |
| A | TYR41 | |
| E | TYR41 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:20850016 |
| Chain | Residue | Details |
| A | SER57 | |
| E | SER57 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711 |
| Chain | Residue | Details |
| A | LYS79 | |
| E | LYS79 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016 |
| Chain | Residue | Details |
| A | THR80 | |
| E | THR80 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER86 | |
| E | SER86 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | THR107 | |
| E | THR107 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297 |
| Chain | Residue | Details |
| A | LYS115 | |
| E | LYS115 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229 |
| Chain | Residue | Details |
| A | LYS122 | |
| E | LYS122 |
| site_id | SWS_FT_FI27 |
| Number of Residues | 2 |
| Details | LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806 |
| Chain | Residue | Details |
| A | LYS18 | |
| E | LYS18 |
