Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7PF3

Nucleosome 4 of the 4x187 nucleosome array containing H1

Functional Information from GO Data

Chain	GOid	namespace	contents
k	0000786	cellular_component	nucleosome
k	0003677	molecular_function	DNA binding
k	0005515	molecular_function	protein binding
k	0005576	cellular_component	extracellular region
k	0005634	cellular_component	nucleus
k	0005654	cellular_component	nucleoplasm
k	0005694	cellular_component	chromosome
k	0006325	biological_process	chromatin organization
k	0006334	biological_process	nucleosome assembly
k	0030527	molecular_function	structural constituent of chromatin
k	0043229	cellular_component	intracellular organelle
k	0046982	molecular_function	protein heterodimerization activity
k	0070062	cellular_component	extracellular exosome
l	0000781	cellular_component	chromosome, telomeric region
l	0000786	cellular_component	nucleosome
l	0003677	molecular_function	DNA binding
l	0003723	molecular_function	RNA binding
l	0005515	molecular_function	protein binding
l	0005576	cellular_component	extracellular region
l	0005634	cellular_component	nucleus
l	0005654	cellular_component	nucleoplasm
l	0005694	cellular_component	chromosome
l	0006325	biological_process	chromatin organization
l	0006334	biological_process	nucleosome assembly
l	0016020	cellular_component	membrane
l	0030527	molecular_function	structural constituent of chromatin
l	0032200	biological_process	telomere organization
l	0032991	cellular_component	protein-containing complex
l	0043505	cellular_component	CENP-A containing nucleosome
l	0045653	biological_process	negative regulation of megakaryocyte differentiation
l	0046982	molecular_function	protein heterodimerization activity
l	0061644	biological_process	protein localization to CENP-A containing chromatin
l	0070062	cellular_component	extracellular exosome
m	0000786	cellular_component	nucleosome
m	0003677	molecular_function	DNA binding
m	0005515	molecular_function	protein binding
m	0005634	cellular_component	nucleus
m	0005694	cellular_component	chromosome
m	0006325	biological_process	chromatin organization
m	0008285	biological_process	negative regulation of cell population proliferation
m	0030527	molecular_function	structural constituent of chromatin
m	0031492	molecular_function	nucleosomal DNA binding
m	0031507	biological_process	heterochromatin formation
m	0043229	cellular_component	intracellular organelle
m	0043505	cellular_component	CENP-A containing nucleosome
m	0046982	molecular_function	protein heterodimerization activity
m	0061644	biological_process	protein localization to CENP-A containing chromatin
m	0070062	cellular_component	extracellular exosome
n	0000786	cellular_component	nucleosome
n	0002227	biological_process	innate immune response in mucosa
n	0003674	molecular_function	molecular_function
n	0003677	molecular_function	DNA binding
n	0005515	molecular_function	protein binding
n	0005615	cellular_component	extracellular space
n	0005634	cellular_component	nucleus
n	0005654	cellular_component	nucleoplasm
n	0005694	cellular_component	chromosome
n	0005829	cellular_component	cytosol
n	0019731	biological_process	antibacterial humoral response
n	0030527	molecular_function	structural constituent of chromatin
n	0031640	biological_process	killing of cells of another organism
n	0042742	biological_process	defense response to bacterium
n	0043229	cellular_component	intracellular organelle
n	0046982	molecular_function	protein heterodimerization activity
n	0050829	biological_process	defense response to Gram-negative bacterium
n	0050830	biological_process	defense response to Gram-positive bacterium
n	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
o	0000786	cellular_component	nucleosome
o	0003677	molecular_function	DNA binding
o	0005515	molecular_function	protein binding
o	0005576	cellular_component	extracellular region
o	0005634	cellular_component	nucleus
o	0005654	cellular_component	nucleoplasm
o	0005694	cellular_component	chromosome
o	0006325	biological_process	chromatin organization
o	0006334	biological_process	nucleosome assembly
o	0030527	molecular_function	structural constituent of chromatin
o	0043229	cellular_component	intracellular organelle
o	0046982	molecular_function	protein heterodimerization activity
o	0070062	cellular_component	extracellular exosome
p	0000781	cellular_component	chromosome, telomeric region
p	0000786	cellular_component	nucleosome
p	0003677	molecular_function	DNA binding
p	0003723	molecular_function	RNA binding
p	0005515	molecular_function	protein binding
p	0005576	cellular_component	extracellular region
p	0005634	cellular_component	nucleus
p	0005654	cellular_component	nucleoplasm
p	0005694	cellular_component	chromosome
p	0006325	biological_process	chromatin organization
p	0006334	biological_process	nucleosome assembly
p	0016020	cellular_component	membrane
p	0030527	molecular_function	structural constituent of chromatin
p	0032200	biological_process	telomere organization
p	0032991	cellular_component	protein-containing complex
p	0043505	cellular_component	CENP-A containing nucleosome
p	0045653	biological_process	negative regulation of megakaryocyte differentiation
p	0046982	molecular_function	protein heterodimerization activity
p	0061644	biological_process	protein localization to CENP-A containing chromatin
p	0070062	cellular_component	extracellular exosome
q	0000786	cellular_component	nucleosome
q	0003677	molecular_function	DNA binding
q	0005515	molecular_function	protein binding
q	0005634	cellular_component	nucleus
q	0005694	cellular_component	chromosome
q	0006325	biological_process	chromatin organization
q	0008285	biological_process	negative regulation of cell population proliferation
q	0030527	molecular_function	structural constituent of chromatin
q	0031492	molecular_function	nucleosomal DNA binding
q	0031507	biological_process	heterochromatin formation
q	0043229	cellular_component	intracellular organelle
q	0043505	cellular_component	CENP-A containing nucleosome
q	0046982	molecular_function	protein heterodimerization activity
q	0061644	biological_process	protein localization to CENP-A containing chromatin
q	0070062	cellular_component	extracellular exosome
r	0000786	cellular_component	nucleosome
r	0002227	biological_process	innate immune response in mucosa
r	0003674	molecular_function	molecular_function
r	0003677	molecular_function	DNA binding
r	0005515	molecular_function	protein binding
r	0005615	cellular_component	extracellular space
r	0005634	cellular_component	nucleus
r	0005654	cellular_component	nucleoplasm
r	0005694	cellular_component	chromosome
r	0005829	cellular_component	cytosol
r	0019731	biological_process	antibacterial humoral response
r	0030527	molecular_function	structural constituent of chromatin
r	0031640	biological_process	killing of cells of another organism
r	0042742	biological_process	defense response to bacterium
r	0043229	cellular_component	intracellular organelle
r	0046982	molecular_function	protein heterodimerization activity
r	0050829	biological_process	defense response to Gram-negative bacterium
r	0050830	biological_process	defense response to Gram-positive bacterium
r	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
s	0000122	biological_process	negative regulation of transcription by RNA polymerase II
s	0000786	cellular_component	nucleosome
s	0000791	cellular_component	euchromatin
s	0000792	cellular_component	heterochromatin
s	0003677	molecular_function	DNA binding
s	0003690	molecular_function	double-stranded DNA binding
s	0003723	molecular_function	RNA binding
s	0005515	molecular_function	protein binding
s	0005634	cellular_component	nucleus
s	0005694	cellular_component	chromosome
s	0006325	biological_process	chromatin organization
s	0006334	biological_process	nucleosome assembly
s	0006357	biological_process	regulation of transcription by RNA polymerase II
s	0030261	biological_process	chromosome condensation
s	0030527	molecular_function	structural constituent of chromatin
s	0031490	molecular_function	chromatin DNA binding
s	0031492	molecular_function	nucleosomal DNA binding
s	0042826	molecular_function	histone deacetylase binding
s	0045910	biological_process	negative regulation of DNA recombination

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
m	ALA21-VAL27

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
l	GLY14-HIS18

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
k	LYS14-LEU20

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
n	ARG92-GLY114

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
k	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P15865

Chain	Residue	Details
s	SER1
r	PRO1

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P43274

Chain	Residue	Details
s	LYS16
r	GLU2

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:17081983, ECO:0007744\|PubMed:18669648, ECO:0007744\|PubMed:18691976, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692, ECO:0007744\|PubMed:23186163, ECO:0007744\|PubMed:24275569

Chain	Residue	Details
s	THR17
r	LYS11
r	LYS15
r	LYS16
r	LYS20
r	LYS23
r	LYS43
r	LYS85
n	LYS11
n	LYS15
n	LYS16
n	LYS20
n	LYS23
n	LYS43
n	LYS85
r	LYS5

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:3782055

Chain	Residue	Details
s	LYS25
r	SER6
q	LYS9
q	LYS95

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P43274

Chain	Residue	Details
s	LYS33
r	LYS12
l	LYS44
p	LYS8
p	LYS16
p	LYS44

site_id	SWS_FT_FI6
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P43274

Chain	Residue	Details
s	SER35
r	SER14
l	LYS77
l	LYS91
p	LYS12
p	LYS31
p	LYS77
p	LYS91

site_id	SWS_FT_FI7
Number of Residues	5
Details	MOD_RES: N6-(beta-hydroxybutyryl)lysine => ECO:0000250\|UniProtKB:P43277

Chain	Residue	Details
s	LYS51
s	LYS63
s	LYS84
s	LYS89
s	LYS105

site_id	SWS_FT_FI8
Number of Residues	1
Details	MOD_RES: Citrulline => ECO:0000250\|UniProtKB:P43274

Chain	Residue	Details
s	ARG53
n	LYS116
n	LYS120
r	LYS34
r	LYS116
r	LYS120

site_id	SWS_FT_FI9
Number of Residues	1
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:20068231

Chain	Residue	Details
s	THR145
r	GLU35
m	LYS125
q	LYS118
q	LYS119
q	LYS125

site_id	SWS_FT_FI10
Number of Residues	1
Details	MOD_RES: ADP-ribosylserine => ECO:0000269\|PubMed:27723750

Chain	Residue	Details
s	SER149
r	SER36
o	LYS14
o	LYS56

site_id	SWS_FT_FI11
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17081983, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:21406692

Chain	Residue	Details
s	SER186
n	LYS108
r	LYS46
r	LYS108

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269\|PubMed:24681537

Chain	Residue	Details
n	LYS57
r	LYS57
q	LYS119

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: Dimethylated arginine => ECO:0000250\|UniProtKB:Q96A08

Chain	Residue	Details
n	ARG79
r	ARG79

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Omega-N-methylarginine => ECO:0000250\|UniProtKB:Q96A08

Chain	Residue	Details
n	ARG86
n	ARG92
r	ARG86
r	ARG92

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000250\|UniProtKB:Q00729

Chain	Residue	Details
n	THR115
r	THR115
p	LYS91

site_id	SWS_FT_FI16
Number of Residues	2
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250\|UniProtKB:P62807

Chain	Residue	Details
n	SER112
r	SER112
l	LYS79
p	LYS20
p	LYS59
p	LYS79

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
n	LYS5
r	LYS5

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
k	SER57
n	LYS120
r	LYS120

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
n	LYS20
r	LYS20

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
n	LYS34
r	LYS34

site_id	SWS_FT_FI21
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250\|UniProtKB:P84243

Chain	Residue	Details
k	SER86
o	SER86

site_id	SWS_FT_FI22
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:19690332

Chain	Residue	Details
k	THR107
o	THR107

site_id	SWS_FT_FI23
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269\|PubMed:31542297

Chain	Residue	Details
k	LYS115
o	LYS115

site_id	SWS_FT_FI24
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269\|PubMed:22389435, ECO:0000269\|PubMed:27436229

Chain	Residue	Details
k	LYS122
o	LYS122

site_id	SWS_FT_FI25
Number of Residues	2
Details	LIPID: N6-decanoyllysine => ECO:0000269\|PubMed:35939806

Chain	Residue	Details
k	LYS18
o	LYS18

site_id	SWS_FT_FI26
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000269\|PubMed:21076176

Chain	Residue	Details
k	ALA110
o	ALA110

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)