2CV5
Crystal structure of human nucleosome core particle
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 | 0043229 | cellular_component | intracellular organelle |
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 | 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 | 0008285 | biological_process | negative regulation of cell population proliferation |
C | 0030527 | molecular_function | structural constituent of chromatin |
C | 0031492 | molecular_function | nucleosomal DNA binding |
C | 0031507 | biological_process | heterochromatin formation |
C | 0043229 | cellular_component | intracellular organelle |
C | 0043505 | cellular_component | CENP-A containing nucleosome |
C | 0046982 | molecular_function | protein heterodimerization activity |
C | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
C | 0070062 | cellular_component | extracellular exosome |
D | 0000786 | cellular_component | nucleosome |
D | 0002227 | biological_process | innate immune response in mucosa |
D | 0003674 | molecular_function | molecular_function |
D | 0003677 | molecular_function | DNA binding |
D | 0005515 | molecular_function | protein binding |
D | 0005615 | cellular_component | extracellular space |
D | 0005634 | cellular_component | nucleus |
D | 0005654 | cellular_component | nucleoplasm |
D | 0005694 | cellular_component | chromosome |
D | 0005829 | cellular_component | cytosol |
D | 0019731 | biological_process | antibacterial humoral response |
D | 0030527 | molecular_function | structural constituent of chromatin |
D | 0031640 | biological_process | killing of cells of another organism |
D | 0042742 | biological_process | defense response to bacterium |
D | 0043229 | cellular_component | intracellular organelle |
D | 0046982 | molecular_function | protein heterodimerization activity |
D | 0050829 | biological_process | defense response to Gram-negative bacterium |
D | 0050830 | biological_process | defense response to Gram-positive bacterium |
D | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
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 | 0043229 | cellular_component | intracellular organelle |
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 | 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 | 0008285 | biological_process | negative regulation of cell population proliferation |
G | 0030527 | molecular_function | structural constituent of chromatin |
G | 0031492 | molecular_function | nucleosomal DNA binding |
G | 0031507 | biological_process | heterochromatin formation |
G | 0043229 | cellular_component | intracellular organelle |
G | 0043505 | cellular_component | CENP-A containing nucleosome |
G | 0046982 | molecular_function | protein heterodimerization activity |
G | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
G | 0070062 | cellular_component | extracellular exosome |
H | 0000786 | cellular_component | nucleosome |
H | 0002227 | biological_process | innate immune response in mucosa |
H | 0003674 | molecular_function | molecular_function |
H | 0003677 | molecular_function | DNA binding |
H | 0005515 | molecular_function | protein binding |
H | 0005615 | cellular_component | extracellular space |
H | 0005634 | cellular_component | nucleus |
H | 0005654 | cellular_component | nucleoplasm |
H | 0005694 | cellular_component | chromosome |
H | 0005829 | cellular_component | cytosol |
H | 0019731 | biological_process | antibacterial humoral response |
H | 0030527 | molecular_function | structural constituent of chromatin |
H | 0031640 | biological_process | killing of cells of another organism |
H | 0042742 | biological_process | defense response to bacterium |
H | 0043229 | cellular_component | intracellular organelle |
H | 0046982 | molecular_function | protein heterodimerization activity |
H | 0050829 | biological_process | defense response to Gram-negative bacterium |
H | 0050830 | biological_process | defense response to Gram-positive bacterium |
H | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN J 1001 |
Chain | Residue |
J | DG185 |
J | DG186 |
J | HOH1043 |
J | HOH1046 |
site_id | AC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN J 1002 |
Chain | Residue |
J | DG267 |
J | HOH1041 |
J | HOH1044 |
J | HOH1071 |
site_id | AC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MN J 1003 |
Chain | Residue |
J | HOH1042 |
J | DG217 |
site_id | AC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MN I 1004 |
Chain | Residue |
I | DG68 |
I | HOH1039 |
J | HOH1081 |
site_id | AC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MN I 1005 |
Chain | Residue |
I | DG121 |
site_id | AC6 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE MN J 1006 |
Chain | Residue |
J | DG280 |
site_id | AC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE MN I 1007 |
Chain | Residue |
I | DG134 |
I | HOH1042 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE MN D 1008 |
Chain | Residue |
D | VAL45 |
D | HOH1026 |
E | ASP77 |
E | HOH2048 |
site_id | AC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE MN J 1009 |
Chain | Residue |
I | HOH1095 |
J | HOH1087 |
J | HOH1088 |
site_id | BC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL C 2001 |
Chain | Residue |
C | GLY46 |
C | ALA47 |
D | THR87 |
D | SER88 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CL G 2002 |
Chain | Residue |
G | GLY44 |
G | ALA45 |
G | GLY46 |
G | ALA47 |
H | THR87 |
H | SER88 |
site_id | BC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL E 2003 |
Chain | Residue |
E | PRO121 |
E | LYS122 |
site_id | BC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL A 2004 |
Chain | Residue |
A | PRO121 |
A | LYS122 |
Functional Information from PROSITE/UniProt
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 | ALA21-VAL27 |
site_id | PS00357 |
Number of Residues | 23 |
Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
Chain | Residue | Details |
D | ARG89-GLY111 |
site_id | PS00322 |
Number of Residues | 7 |
Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
Chain | Residue | Details |
A | LYS14-LEU20 |
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 | GLU-1 | |
H | GLU-1 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | MOD_RES: ADP-ribosyl glutamic acid => ECO:0000269|PubMed:27530147 |
Chain | Residue | Details |
D | PRO0 | |
H | PRO0 |
site_id | SWS_FT_FI3 |
Number of Residues | 16 |
Details | MOD_RES: N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732 |
Chain | Residue | Details |
D | SER3 | |
H | LYS9 | |
H | LYS13 | |
H | ALA14 | |
H | ALA18 | |
H | LYS21 | |
H | VAL41 | |
H | ARG83 | |
D | LYS9 | |
D | LYS13 | |
D | ALA14 | |
D | ALA18 | |
D | LYS21 | |
D | VAL41 | |
D | ARG83 | |
H | SER3 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | MOD_RES: ADP-ribosylserine => ECO:0000269|PubMed:34874266 |
Chain | Residue | Details |
D | ALA4 | |
H | ALA4 | |
G | ALA10 | |
G | LEU96 |
site_id | SWS_FT_FI5 |
Number of Residues | 2 |
Details | MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322 |
Chain | Residue | Details |
D | GLY10 | |
H | GLY10 | |
B | ARG45 | |
F | GLY9 | |
F | ARG17 | |
F | ARG45 |
site_id | SWS_FT_FI6 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711 |
Chain | Residue | Details |
D | LYS12 | |
H | LYS12 | |
B | ARG78 | |
B | ARG92 | |
F | GLY13 | |
F | PRO32 | |
F | ARG78 | |
F | ARG92 |
site_id | SWS_FT_FI7 |
Number of Residues | 2 |
Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537 |
Chain | Residue | Details |
D | ASP22 | |
H | ASP22 | |
G | LYS75 | |
G | THR76 |
site_id | SWS_FT_FI8 |
Number of Residues | 6 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435 |
Chain | Residue | Details |
D | GLU32 | |
D | ALA114 | |
D | TYR118 | |
H | GLU32 | |
H | ALA114 | |
H | TYR118 |
site_id | SWS_FT_FI9 |
Number of Residues | 2 |
Details | MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475 |
Chain | Residue | Details |
D | SER33 | |
H | SER33 | |
C | ALA126 | |
G | LYS119 | |
G | THR120 | |
G | ALA126 |
site_id | SWS_FT_FI10 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q8CGP1 |
Chain | Residue | Details |
D | TYR34 | |
H | TYR34 | |
E | ALA15 | |
E | SER57 |
site_id | SWS_FT_FI11 |
Number of Residues | 4 |
Details | MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869 |
Chain | Residue | Details |
D | GLN44 | |
D | HIS106 | |
H | GLN44 | |
H | HIS106 |
site_id | SWS_FT_FI12 |
Number of Residues | 2 |
Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537 |
Chain | Residue | Details |
D | ALA55 | |
H | ALA55 | |
E | GLN19 | |
G | THR120 |
site_id | SWS_FT_FI13 |
Number of Residues | 2 |
Details | MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08 |
Chain | Residue | Details |
D | LEU77 | |
H | LEU77 |
site_id | SWS_FT_FI14 |
Number of Residues | 4 |
Details | MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08 |
Chain | Residue | Details |
D | SER84 | |
D | GLU90 | |
H | SER84 | |
H | GLU90 |
site_id | SWS_FT_FI15 |
Number of Residues | 2 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729 |
Chain | Residue | Details |
D | LYS113 | |
H | LYS113 | |
F | ARG92 |
site_id | SWS_FT_FI16 |
Number of Residues | 2 |
Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807 |
Chain | Residue | Details |
D | GLU110 | |
H | GLU110 | |
B | THR80 | |
F | VAL21 | |
F | VAL60 | |
F | THR80 |
site_id | SWS_FT_FI17 |
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 | SER3 | |
H | SER3 |
site_id | SWS_FT_FI18 |
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:16627869, ECO:0000269|PubMed:16713563 |
Chain | Residue | Details |
A | PRO38 | |
D | TYR118 | |
H | TYR118 |
site_id | SWS_FT_FI19 |
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 | ALA18 | |
H | ALA18 |
site_id | SWS_FT_FI20 |
Number of Residues | 2 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816 |
Chain | Residue | Details |
D | GLU32 | |
H | GLU32 |
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 | THR80 | |
E | THR80 |
site_id | SWS_FT_FI22 |
Number of Residues | 2 |
Details | MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016 |
Chain | Residue | Details |
A | ASP81 | |
E | ASP81 |
site_id | SWS_FT_FI23 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
Chain | Residue | Details |
A | SER87 | |
E | SER87 |
site_id | SWS_FT_FI24 |
Number of Residues | 2 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3 |
Chain | Residue | Details |
A | ASN108 | |
E | ASN108 |
site_id | SWS_FT_FI25 |
Number of Residues | 2 |
Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297 |
Chain | Residue | Details |
A | ARG116 | |
E | ARG116 |
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 | ASP123 | |
E | ASP123 |
site_id | SWS_FT_FI27 |
Number of Residues | 2 |
Details | LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806 |
Chain | Residue | Details |
A | GLN19 | |
E | GLN19 |