8YBJ

Cryo-EM structure of human nucleosome core particle composed of the Widom 601 DNA sequence

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	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	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	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	0031507	biological_process	heterochromatin formation
C	0043505	cellular_component	CENP-A containing nucleosome
C	0061644	biological_process	protein localization to CENP-A containing chromatin
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
D	0001530	molecular_function	lipopolysaccharide binding
D	0002227	biological_process	innate immune response in mucosa
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	0005886	cellular_component	plasma membrane
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
D	0019731	biological_process	antibacterial humoral response
D	0031640	biological_process	killing of cells of another organism
D	0042742	biological_process	defense response to bacterium
D	0043505	cellular_component	CENP-A containing nucleosome
D	0050829	biological_process	defense response to Gram-negative bacterium
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061644	biological_process	protein localization to CENP-A containing chromatin
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	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	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	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	0031507	biological_process	heterochromatin formation
G	0043505	cellular_component	CENP-A containing nucleosome
G	0061644	biological_process	protein localization to CENP-A containing chromatin
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
H	0001530	molecular_function	lipopolysaccharide binding
H	0002227	biological_process	innate immune response in mucosa
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	0005886	cellular_component	plasma membrane
H	0006325	biological_process	chromatin organization
H	0006334	biological_process	nucleosome assembly
H	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
H	0019731	biological_process	antibacterial humoral response
H	0031640	biological_process	killing of cells of another organism
H	0042742	biological_process	defense response to bacterium
H	0043505	cellular_component	CENP-A containing nucleosome
H	0050829	biological_process	defense response to Gram-negative bacterium
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061644	biological_process	protein localization to CENP-A containing chromatin
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide

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: Phosphoserine; by RPS6KA5 => ECO:0000269|PubMed:11709551, ECO:0000269|PubMed:15010469

Chain	Residue	Details
C	SER1
G	SER1

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250|UniProtKB:C0HKE1

Chain	Residue	Details
C	ARG3
G	ARG3

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:C0HKE1

Chain	Residue	Details
C	LYS5
H	LYS11
H	LYS15
H	LYS16
H	LYS20
H	LYS23
H	LYS43
H	LYS85
G	LYS5
D	LYS15
D	LYS16
D	LYS20
D	LYS23
D	LYS43
D	LYS85
H	LYS5

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435

Chain	Residue	Details
C	LYS9
C	LYS95
G	LYS9
G	LYS95

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: N6-(beta-hydroxybutyryl)lysine; alternate => ECO:0000269|PubMed:27105115

Chain	Residue	Details
C	LYS13
G	LYS13
B	LYS44
F	LYS8
F	LYS16
F	LYS44

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322

Chain	Residue	Details
C	LYS36
G	LYS36
B	LYS77
B	LYS91
F	LYS12
F	LYS31
F	LYS77
F	LYS91

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537

Chain	Residue	Details
C	LYS74
C	LYS75
G	LYS74
G	LYS75

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N5-methylglutamine => ECO:0000269|PubMed:24352239

Chain	Residue	Details
C	GLN104
G	GLN104
D	LYS120
H	LYS34
H	LYS116
H	LYS120

---

site_id	SWS_FT_FI9
Number of Residues	6
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
C	LYS118
C	LYS119
C	LYS125
G	LYS118
G	LYS119
G	LYS125

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by DCAF1 => ECO:0000269|PubMed:15078818, ECO:0000269|PubMed:24140421

Chain	Residue	Details
C	THR120
G	THR120
E	LYS14
E	LYS56

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:22713238, ECO:0000269|PubMed:22980979

Chain	Residue	Details
C	LYS13
G	LYS13
H	LYS46
H	LYS108

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:15386022, ECO:0000269|PubMed:16359901, ECO:0000269|PubMed:16702407, ECO:0000269|PubMed:25470042

Chain	Residue	Details
B	THR80
C	LYS119
E	LYS18
G	LYS119

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:22713238, ECO:0000269|PubMed:22980979

Chain	Residue	Details
C	LYS15
G	LYS15

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:25218447

Chain	Residue	Details
B	LYS12
F	LYS12
H	ARG86
H	ARG92

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:19818714

Chain	Residue	Details
A	LYS27
B	LYS91
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
H	LYS120

---

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

---