5GT3
Crystal structure of nucleosome particle in the presence of human testis-specific histone variant, hTh2b
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 | 0000786 | cellular_component | nucleosome |
C | 0003674 | molecular_function | molecular_function |
C | 0003677 | molecular_function | DNA binding |
C | 0005634 | cellular_component | nucleus |
C | 0005694 | cellular_component | chromosome |
C | 0008150 | biological_process | biological_process |
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 | 0000786 | cellular_component | nucleosome |
G | 0003674 | molecular_function | molecular_function |
G | 0003677 | molecular_function | DNA binding |
G | 0005634 | cellular_component | nucleus |
G | 0005694 | cellular_component | chromosome |
G | 0008150 | biological_process | biological_process |
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 MN E 201 |
Chain | Residue |
C | GLU64 |
D | VAL48 |
D | HOH201 |
E | ASP77 |
site_id | AC2 |
Number of Residues | 4 |
Details | binding site for residue MN G 201 |
Chain | Residue |
G | GLY44 |
G | ALA45 |
G | GLY46 |
H | SER91 |
site_id | AC3 |
Number of Residues | 1 |
Details | binding site for residue MN I 202 |
Chain | Residue |
I | DG68 |
site_id | AC4 |
Number of Residues | 1 |
Details | binding site for residue MN I 203 |
Chain | Residue |
I | DG78 |
site_id | AC5 |
Number of Residues | 2 |
Details | binding site for residue CL I 204 |
Chain | Residue |
I | DT120 |
I | DG121 |
site_id | AC6 |
Number of Residues | 1 |
Details | binding site for residue CL I 205 |
Chain | Residue |
I | DG100 |
site_id | AC7 |
Number of Residues | 1 |
Details | binding site for residue MN J 301 |
Chain | Residue |
J | DG280 |
site_id | AC8 |
Number of Residues | 1 |
Details | binding site for residue MN J 302 |
Chain | Residue |
J | DG217 |
site_id | AC9 |
Number of Residues | 2 |
Details | binding site for residue MN J 304 |
Chain | Residue |
J | DG267 |
J | DG268 |
site_id | AD1 |
Number of Residues | 1 |
Details | binding site for residue MN J 305 |
Chain | Residue |
J | DG246 |
site_id | AD2 |
Number of Residues | 1 |
Details | binding site for residue MN J 307 |
Chain | Residue |
J | DC172 |
site_id | AD3 |
Number of Residues | 2 |
Details | binding site for residue CL J 308 |
Chain | Residue |
J | DG283 |
J | DG284 |
site_id | AD4 |
Number of Residues | 2 |
Details | binding site for residue CL J 309 |
Chain | Residue |
J | DG185 |
J | DG186 |
site_id | AD5 |
Number of Residues | 1 |
Details | binding site for residue CL J 310 |
Chain | Residue |
J | DA173 |
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 | 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 | 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 | PRO0 | |
H | PRO0 |
site_id | SWS_FT_FI2 |
Number of Residues | 16 |
Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732 |
Chain | Residue | Details |
D | LYS5 | |
H | LYS11 | |
H | LYS15 | |
H | LYS16 | |
H | LYS20 | |
H | LYS23 | |
H | LYS43 | |
H | LYS85 | |
D | LYS11 | |
D | LYS15 | |
D | LYS16 | |
D | LYS20 | |
D | LYS23 | |
D | LYS43 | |
D | LYS85 | |
H | LYS5 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322 |
Chain | Residue | Details |
D | LYS12 | |
H | LYS12 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P33778 |
Chain | Residue | Details |
D | LYS34 | |
D | LYS116 | |
D | LYS120 | |
H | LYS34 | |
H | LYS116 | |
H | LYS120 |
site_id | SWS_FT_FI5 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q64475 |
Chain | Residue | Details |
D | SER36 | |
H | SER36 | |
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 | LYS46 | |
D | LYS108 | |
H | LYS46 | |
H | LYS108 | |
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 | LYS57 | |
H | LYS57 | |
G | LYS74 | |
G | LYS75 |
site_id | SWS_FT_FI8 |
Number of Residues | 2 |
Details | MOD_RES: Dimethylated arginine => ECO:0000269|PubMed:21249133 |
Chain | Residue | Details |
D | ARG79 | |
H | ARG79 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000269|PubMed:21249133 |
Chain | Residue | Details |
D | SER84 | |
H | SER84 |
site_id | SWS_FT_FI10 |
Number of Residues | 4 |
Details | MOD_RES: Omega-N-methylarginine => ECO:0000269|PubMed:21249133 |
Chain | Residue | Details |
D | ARG86 | |
D | ARG92 | |
H | ARG86 | |
H | ARG92 | |
G | LYS119 | |
G | LYS125 |
site_id | SWS_FT_FI11 |
Number of Residues | 2 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729 |
Chain | Residue | Details |
D | THR115 | |
H | THR115 |
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 | LYS5 | |
H | LYS5 | |
E | LYS18 | |
E | LYS64 |
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 | LYS120 | |
H | LYS120 |
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 | LYS20 | |
H | LYS20 |
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 | LYS34 | |
H | LYS34 | |
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 |