1ID3
CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000500 | cellular_component | RNA polymerase I upstream activating factor complex |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005694 | cellular_component | chromosome |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006355 | biological_process | regulation of DNA-templated transcription |
| A | 0006878 | biological_process | intracellular copper ion homeostasis |
| A | 0008823 | molecular_function | cupric reductase (NADH) activity |
| A | 0009060 | biological_process | aerobic respiration |
| A | 0009303 | biological_process | rRNA transcription |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0042790 | biological_process | nucleolar large rRNA transcription by RNA polymerase I |
| A | 0043505 | cellular_component | CENP-A containing nucleosome |
| A | 0043935 | biological_process | sexual sporulation resulting in formation of a cellular spore |
| A | 0045943 | biological_process | positive regulation of transcription by RNA polymerase I |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| A | 0070911 | biological_process | global genome nucleotide-excision repair |
| B | 0000500 | cellular_component | RNA polymerase I upstream activating factor complex |
| 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 | 0006325 | biological_process | chromatin organization |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0006355 | biological_process | regulation of DNA-templated transcription |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0042790 | biological_process | nucleolar large rRNA transcription by RNA polymerase I |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0045943 | biological_process | positive regulation of transcription by RNA polymerase I |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0006281 | biological_process | DNA repair |
| C | 0006325 | biological_process | chromatin organization |
| C | 0006974 | biological_process | DNA damage response |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0031507 | biological_process | heterochromatin formation |
| 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 | 0006325 | biological_process | chromatin organization |
| D | 0006355 | biological_process | regulation of DNA-templated transcription |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0000500 | cellular_component | RNA polymerase I upstream activating factor complex |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005634 | cellular_component | nucleus |
| E | 0005694 | cellular_component | chromosome |
| E | 0006325 | biological_process | chromatin organization |
| E | 0006355 | biological_process | regulation of DNA-templated transcription |
| E | 0006878 | biological_process | intracellular copper ion homeostasis |
| E | 0008823 | molecular_function | cupric reductase (NADH) activity |
| E | 0009060 | biological_process | aerobic respiration |
| E | 0009303 | biological_process | rRNA transcription |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0042790 | biological_process | nucleolar large rRNA transcription by RNA polymerase I |
| E | 0043505 | cellular_component | CENP-A containing nucleosome |
| E | 0043935 | biological_process | sexual sporulation resulting in formation of a cellular spore |
| E | 0045943 | biological_process | positive regulation of transcription by RNA polymerase I |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0070911 | biological_process | global genome nucleotide-excision repair |
| F | 0000500 | cellular_component | RNA polymerase I upstream activating factor complex |
| 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 | 0006325 | biological_process | chromatin organization |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0006355 | biological_process | regulation of DNA-templated transcription |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0042790 | biological_process | nucleolar large rRNA transcription by RNA polymerase I |
| F | 0042802 | molecular_function | identical protein binding |
| F | 0045943 | biological_process | positive regulation of transcription by RNA polymerase I |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005515 | molecular_function | protein binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0006281 | biological_process | DNA repair |
| G | 0006325 | biological_process | chromatin organization |
| G | 0006974 | biological_process | DNA damage response |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0031507 | biological_process | heterochromatin formation |
| 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 | 0006325 | biological_process | chromatin organization |
| H | 0006355 | biological_process | regulation of DNA-templated transcription |
| 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 MN H 131 |
| Chain | Residue |
| G | GLY45 |
| G | SER46 |
| G | GLY47 |
| H | SER93 |
| H | ALA94 |
| site_id | AC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN C 132 |
| Chain | Residue |
| C | ARG89 |
| site_id | AC3 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN J 103 |
| Chain | Residue |
| J | DG267 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 147 |
| Chain | Residue |
| I | DA133 |
| I | DG134 |
| site_id | AC5 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 148 |
| Chain | Residue |
| I | DG70 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN G 132 |
| Chain | Residue |
| G | ASP91 |
| G | GLU93 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE MN I 149 |
| Chain | Residue |
| I | DG121 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 108 |
| Chain | Residue |
| J | DA279 |
| J | DG280 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN E 136 |
| Chain | Residue |
| E | ARG49 |
| I | DT8 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN C 133 |
| Chain | Residue |
| C | ASP91 |
| C | GLU93 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 111 |
| Chain | Residue |
| J | DG216 |
| J | DG217 |
| site_id | BC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN I 150 |
| Chain | Residue |
| I | DG78 |
| J | DG214 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 113 |
| Chain | Residue |
| C | ASP73 |
| J | DC168 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 114 |
| Chain | Residue |
| I | DT45 |
| J | DG246 |
| site_id | BC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MN J 115 |
| Chain | Residue |
| J | DT184 |
| J | DG185 |
| J | DG186 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN D 131 |
| Chain | Residue |
| D | GLU108 |
| D | HIS112 |
| G | GLU65 |
| H | HIS52 |
| site_id | BC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MN J 117 |
| Chain | Residue |
| J | DA202 |
| J | DA203 |
Functional Information from PROSITE/UniProt
| site_id | PS00014 |
| Number of Residues | 4 |
| Details | ER_TARGET Endoplasmic reticulum targeting sequence. SQEL |
| Chain | Residue | Details |
| C | SER128-LEU131 |
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLtFPV |
| Chain | Residue | Details |
| C | ALA22-VAL28 |
| 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. REIQTavRlILpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG95-GLY117 |
| 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 | Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 9 |
| Details | Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Omega-N-methylarginine","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"16768447","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-glutaryllysine","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Site: {"description":"Not ubiquitinated","evidences":[{"source":"PubMed","id":"10642555","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2201907","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N5-methylglutamine","evidences":[{"source":"PubMed","id":"24352239","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI14 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"12535538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12535539","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14660635","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15280549","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |






