1EQZ
X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005694 | cellular_component | chromosome |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0031492 | molecular_function | nucleosomal DNA binding |
| A | 0031507 | biological_process | heterochromatin formation |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005694 | cellular_component | chromosome |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0044877 | molecular_function | protein-containing complex binding |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| C | 0000785 | cellular_component | chromatin |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0003682 | molecular_function | chromatin binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0010467 | biological_process | gene expression |
| 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 | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005694 | cellular_component | chromosome |
| D | 0006334 | biological_process | nucleosome assembly |
| 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 | 0005634 | cellular_component | nucleus |
| E | 0005694 | cellular_component | chromosome |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0031492 | molecular_function | nucleosomal DNA binding |
| E | 0031507 | biological_process | heterochromatin formation |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0005634 | cellular_component | nucleus |
| F | 0005694 | cellular_component | chromosome |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0044877 | molecular_function | protein-containing complex binding |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| G | 0000785 | cellular_component | chromatin |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0003682 | molecular_function | chromatin binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0010467 | biological_process | gene expression |
| 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 | 0005634 | cellular_component | nucleus |
| H | 0005654 | cellular_component | nucleoplasm |
| H | 0005694 | cellular_component | chromosome |
| H | 0006334 | biological_process | nucleosome assembly |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0046982 | molecular_function | protein heterodimerization activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 449 |
| Chain | Residue |
| A | GLY44 |
| A | GLY46 |
| A | ALA47 |
| B | THR90 |
| B | SER91 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL E 450 |
| Chain | Residue |
| F | SER91 |
| E | GLY44 |
| E | GLY46 |
| E | ALA47 |
| F | THR90 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE CAC G 451 |
| Chain | Residue |
| A | GLU64 |
| B | GLN47 |
| B | VAL48 |
| B | HIS49 |
| G | GLU73 |
| G | GLN76 |
| G | ASP77 |
| H | LEU22 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE K J 452 |
| Chain | Residue |
| J | DA255 |
| J | DA256 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE K J 453 |
| Chain | Residue |
| A | LYS124 |
| J | DG216 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE K J 454 |
| Chain | Residue |
| J | DG217 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE K J 455 |
| Chain | Residue |
| J | DG227 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE K J 456 |
| Chain | Residue |
| J | DA228 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE K J 457 |
| Chain | Residue |
| J | DA175 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE K I 458 |
| Chain | Residue |
| I | DG97 |
| I | DG98 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN J 459 |
| Chain | Residue |
| J | DG280 |
| J | HOH500 |
| J | HOH507 |
| site_id | BC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 460 |
| Chain | Residue |
| I | DG134 |
| I | HOH505 |
| site_id | BC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 461 |
| Chain | Residue |
| I | HOH509 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN J 462 |
| Chain | Residue |
| I | DT140 |
| I | HOH511 |
| J | DG246 |
| site_id | BC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 463 |
| Chain | Residue |
| I | DG121 |
| I | HOH513 |
| site_id | BC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 464 |
| Chain | Residue |
| I | DG70 |
| I | DG71 |
| site_id | BC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN I 465 |
| Chain | Residue |
| I | DG39 |
| I | DG40 |
| I | HOH514 |
| site_id | BC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN I 466 |
| Chain | Residue |
| I | DG137 |
| I | DG138 |
| I | HOH488 |
| site_id | CC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 467 |
| Chain | Residue |
| J | DG185 |
| J | DG186 |
| site_id | CC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 468 |
| Chain | Residue |
| J | DG267 |
| J | HOH503 |
| site_id | CC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 469 |
| Chain | Residue |
| J | DA147 |
| site_id | CC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 470 |
| Chain | Residue |
| I | DG100 |
| site_id | CC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 471 |
| Chain | Residue |
| I | DA1 |
| site_id | CC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 472 |
| Chain | Residue |
| I | DA17 |
| I | DG18 |
| site_id | CC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 473 |
| Chain | Residue |
| I | DA124 |
| I | DG125 |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| A | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| D | GLY14-HIS18 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| C | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| B | ARG92-GLY114 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| C | PRO66-ILE74 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | DNA_BIND: |
| Chain | Residue | Details |
| D | LYS16-LYS20 | |
| H | LYS16-LYS20 | |
| B | LYS16 | |
| B | THR21 | |
| F | SER6 | |
| F | GLY13 | |
| F | LYS16 | |
| F | THR21 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | SER1 | |
| H | SER1 | |
| G | ARG2 | |
| G | ARG17 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Symmetric dimethylarginine; by PRMT5 and PRMT7; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | ARG3 | |
| H | ARG3 | |
| E | ALA10 | |
| E | LEU96 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS5 | |
| H | LYS5 | |
| F | TYR121 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-propionyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS8 | |
| D | LYS16 | |
| D | LYS44 | |
| D | LYS79 | |
| H | LYS8 | |
| H | LYS16 | |
| H | LYS44 | |
| H | LYS79 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS12 | |
| D | LYS20 | |
| H | LYS12 | |
| H | LYS20 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS31 | |
| D | LYS91 | |
| H | LYS31 | |
| H | LYS91 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; by PAK2 => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | SER47 | |
| H | SER47 | |
| E | LYS119 | |
| E | THR120 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | TYR51 | |
| D | TYR88 | |
| H | TYR51 | |
| H | TYR88 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS59 | |
| H | LYS59 | |
| E | THR120 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS77 | |
| H | LYS77 | |
| C | LYS64 | |
| G | LYS18 | |
| G | LYS23 | |
| G | LYS64 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250|UniProtKB:P62805 |
| Chain | Residue | Details |
| D | LYS31 | |
| H | 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 |
| C | LYS27 | |
| D | LYS91 | |
| G | LYS27 | |
| H | LYS91 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | SER28 | |
| G | SER28 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P68431 |
| Chain | Residue | Details |
| C | LYS37 | |
| G | LYS37 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | TYR41 | |
| G | TYR41 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| C | LYS56 | |
| C | LYS79 | |
| G | LYS56 | |
| G | LYS79 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | SER57 | |
| G | SER57 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | THR80 | |
| C | THR107 | |
| G | THR80 | |
| G | THR107 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| C | SER86 | |
| G | SER86 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | LYS115 | |
| G | LYS115 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | LYS122 | |
| G | LYS122 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| C | CYS110 | |
| G | CYS110 |
