1F66
2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLE CONTAINING THE VARIANT HISTONE H2A.Z
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 | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0043505 | cellular_component | CENP-A containing nucleosome |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| C | 0000786 | cellular_component | nucleosome |
| C | 0000791 | cellular_component | euchromatin |
| C | 0000792 | cellular_component | heterochromatin |
| C | 0000978 | molecular_function | RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| C | 0000979 | molecular_function | RNA polymerase II core promoter sequence-specific DNA binding |
| C | 0001740 | cellular_component | Barr body |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005515 | molecular_function | protein 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 | 0031490 | molecular_function | chromatin DNA binding |
| C | 0031492 | molecular_function | nucleosomal DNA binding |
| C | 0043229 | cellular_component | intracellular organelle |
| C | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0070062 | cellular_component | extracellular exosome |
| C | 0070828 | biological_process | heterochromatin organization |
| C | 0071392 | biological_process | cellular response to estradiol stimulus |
| 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 | 0005654 | cellular_component | nucleoplasm |
| F | 0005694 | cellular_component | chromosome |
| F | 0006325 | biological_process | chromatin organization |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0043505 | cellular_component | CENP-A containing nucleosome |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| G | 0000786 | cellular_component | nucleosome |
| G | 0000791 | cellular_component | euchromatin |
| G | 0000792 | cellular_component | heterochromatin |
| G | 0000978 | molecular_function | RNA polymerase II cis-regulatory region sequence-specific DNA binding |
| G | 0000979 | molecular_function | RNA polymerase II core promoter sequence-specific DNA binding |
| G | 0001740 | cellular_component | Barr body |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005515 | molecular_function | protein 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 | 0031490 | molecular_function | chromatin DNA binding |
| G | 0031492 | molecular_function | nucleosomal DNA binding |
| G | 0043229 | cellular_component | intracellular organelle |
| G | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0070062 | cellular_component | extracellular exosome |
| G | 0070828 | biological_process | heterochromatin organization |
| G | 0071392 | biological_process | cellular response to estradiol stimulus |
| 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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MN E 1001 |
| Chain | Residue |
| D | VAL1245 |
| E | HOH240 |
| E | HOH241 |
| E | HOH242 |
| E | ASP677 |
| F | HOH327 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN I 1002 |
| Chain | Residue |
| I | DG39 |
| I | DG40 |
| I | HOH1022 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 1003 |
| Chain | Residue |
| I | DG70 |
| I | DG71 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 1004 |
| Chain | Residue |
| I | DA99 |
| I | DG100 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 1005 |
| Chain | Residue |
| I | DG121 |
| I | HOH1060 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 1006 |
| Chain | Residue |
| I | DG134 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN I 1007 |
| Chain | Residue |
| I | DG137 |
| I | DG138 |
| I | HOH1027 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 1008 |
| Chain | Residue |
| J | DG185 |
| J | DG186 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 1010 |
| Chain | Residue |
| J | DG217 |
| site_id | BC1 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 1011 |
| Chain | Residue |
| J | DG246 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 1012 |
| Chain | Residue |
| J | DG267 |
| J | DG268 |
| site_id | BC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 1013 |
| Chain | Residue |
| J | DG280 |
| J | HOH1059 |
| site_id | BC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN C 1014 |
| Chain | Residue |
| C | HOH104 |
| C | HIS912 |
| C | HIS914 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN G 1128 |
| Chain | Residue |
| G | HIS1112 |
| G | HIS1114 |
Functional Information from PROSITE/UniProt
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG1289-GLY1311 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| B | GLY14-HIS18 |
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA823-VAL829 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS414-LEU420 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO466-ILE474 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | MOD_RES: Citrulline; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | ARG402 | |
| A | ARG417 | |
| E | ARG602 | |
| E | ARG617 | |
| H | SER1403 | |
| H | GLY1410 | |
| H | LYS1413 | |
| H | THR1418 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine; by HASPIN => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | THR403 | |
| E | THR603 | |
| G | ALA1012 | |
| G | THR1014 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:12138181 |
| Chain | Residue | Details |
| A | LYS404 | |
| E | LYS604 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | GLN405 | |
| E | GLN605 | |
| H | TYR1518 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine; by PKC => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | THR411 | |
| E | THR606 | |
| E | THR611 | |
| F | LYS216 | |
| F | LYS244 | |
| A | THR406 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250 |
| Chain | Residue | Details |
| A | ARG408 | |
| E | ARG608 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000305|PubMed:12138181 |
| Chain | Residue | Details |
| A | LYS409 | |
| E | LYS609 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| B | LYS79 | |
| F | LYS277 | |
| F | LYS279 | |
| A | SER410 | |
| E | SER610 | |
| F | LYS231 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| A | LYS414 | |
| E | LYS614 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 10 |
| Details | MOD_RES: N6-methyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS427 | |
| A | LYS436 | |
| A | LYS464 | |
| E | LYS618 | |
| E | LYS623 | |
| E | LYS627 | |
| E | LYS636 | |
| E | LYS664 | |
| A | LYS418 | |
| A | LYS423 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: Citrulline => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | ARG426 | |
| E | ARG626 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | SER428 | |
| E | SER628 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P68431 |
| Chain | Residue | Details |
| A | LYS437 | |
| E | LYS637 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | TYR441 | |
| E | TYR641 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P84228 |
| Chain | Residue | Details |
| F | LYS212 | |
| F | LYS220 | |
| F | LYS259 | |
| F | LYS279 | |
| A | LYS456 | |
| A | LYS479 | |
| E | LYS656 | |
| E | LYS679 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| F | LYS291 | |
| A | SER457 | |
| E | SER657 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| E | THR680 | |
| E | THR707 | |
| A | THR480 | |
| A | THR507 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER486 | |
| E | SER686 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS515 | |
| E | LYS715 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | LYS522 | |
| E | LYS722 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:Q71DI3 |
| Chain | Residue | Details |
| A | CYS510 | |
| E | CYS710 |
