8KB5

Cryo-EM structure of the human nucleosome containing H3.8

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000775	cellular_component	chromosome, centromeric region
A	0000781	cellular_component	chromosome, telomeric region
A	0000785	cellular_component	chromatin
A	0000786	cellular_component	nucleosome
A	0000939	cellular_component	inner kinetochore
A	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
A	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
A	0001556	biological_process	oocyte maturation
A	0001649	biological_process	osteoblast differentiation
A	0001740	cellular_component	Barr body
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	0006334	biological_process	nucleosome assembly
A	0006997	biological_process	nucleus organization
A	0007283	biological_process	spermatogenesis
A	0007286	biological_process	spermatid development
A	0007338	biological_process	single fertilization
A	0007566	biological_process	embryo implantation
A	0008283	biological_process	cell population proliferation
A	0008584	biological_process	male gonad development
A	0030307	biological_process	positive regulation of cell growth
A	0030527	molecular_function	structural constituent of chromatin
A	0031492	molecular_function	nucleosomal DNA binding
A	0031508	biological_process	pericentric heterochromatin formation
A	0031509	biological_process	subtelomeric heterochromatin formation
A	0032200	biological_process	telomere organization
A	0032991	cellular_component	protein-containing complex
A	0035264	biological_process	multicellular organism growth
A	0042692	biological_process	muscle cell differentiation
A	0046982	molecular_function	protein heterodimerization activity
A	0048477	biological_process	oogenesis
A	0070062	cellular_component	extracellular exosome
A	0090230	biological_process	regulation of centromere complex assembly
A	1902340	biological_process	negative regulation of chromosome condensation
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	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	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	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	0043505	cellular_component	CENP-A containing nucleosome
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	0061644	biological_process	protein localization to CENP-A containing chromatin
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
E	0000775	cellular_component	chromosome, centromeric region
E	0000781	cellular_component	chromosome, telomeric region
E	0000785	cellular_component	chromatin
E	0000786	cellular_component	nucleosome
E	0000939	cellular_component	inner kinetochore
E	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
E	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
E	0001556	biological_process	oocyte maturation
E	0001649	biological_process	osteoblast differentiation
E	0001740	cellular_component	Barr body
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	0006334	biological_process	nucleosome assembly
E	0006997	biological_process	nucleus organization
E	0007283	biological_process	spermatogenesis
E	0007286	biological_process	spermatid development
E	0007338	biological_process	single fertilization
E	0007566	biological_process	embryo implantation
E	0008283	biological_process	cell population proliferation
E	0008584	biological_process	male gonad development
E	0030307	biological_process	positive regulation of cell growth
E	0030527	molecular_function	structural constituent of chromatin
E	0031492	molecular_function	nucleosomal DNA binding
E	0031508	biological_process	pericentric heterochromatin formation
E	0031509	biological_process	subtelomeric heterochromatin formation
E	0032200	biological_process	telomere organization
E	0032991	cellular_component	protein-containing complex
E	0035264	biological_process	multicellular organism growth
E	0042692	biological_process	muscle cell differentiation
E	0046982	molecular_function	protein heterodimerization activity
E	0048477	biological_process	oogenesis
E	0070062	cellular_component	extracellular exosome
E	0090230	biological_process	regulation of centromere complex assembly
E	1902340	biological_process	negative regulation of chromosome condensation
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	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	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	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	0043505	cellular_component	CENP-A containing nucleosome
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	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	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	SITE: Interaction with ZMYND11 => ECO:0000269|PubMed:24590075

Chain	Residue	Details
A	SER31
E	SER31

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Citrulline; alternate => ECO:0000269|PubMed:16567635

Chain	Residue	Details
A	ARG2
E	ARG2

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by HASPIN and VRK1 => ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:31527692

Chain	Residue	Details
A	THR3
H	LYS11
H	LYS15
H	LYS16
H	LYS20
H	LYS23
H	LYS43
H	LYS85
E	THR3
D	LYS15
D	LYS16
D	LYS20
D	LYS23
D	LYS43
D	LYS85
H	LYS5

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708

Chain	Residue	Details
A	ARG4
E	ARG4
G	LYS9
G	LYS95

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: 5-glutamyl serotonin; alternate => ECO:0000269|PubMed:30867594

Chain	Residue	Details
A	TRP5
E	TRP5
B	LYS44
F	LYS8
F	LYS16
F	LYS44

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by PKC => ECO:0000269|PubMed:20228790

Chain	Residue	Details
A	THR6
E	THR6
B	LYS77
B	LYS91
F	LYS12
F	LYS31
F	LYS77
F	LYS91

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Symmetric dimethylarginine; by PRMT5; alternate => ECO:0000250|UniProtKB:P84244

Chain	Residue	Details
A	ARG8
E	ARG8
G	LYS74
G	LYS75

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:11242053, ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:16457588, ECO:0000269|PubMed:17194708, ECO:0000269|PubMed:7309716

Chain	Residue	Details
A	LYS9
E	LYS9
D	LYS120
H	LYS34
H	LYS116
H	LYS120

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:15851689, ECO:0000269|PubMed:16185088

Chain	Residue	Details
A	SER10
E	SER10
C	LYS125
G	LYS118
G	LYS119
G	LYS125

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphothreonine; by PKC => ECO:0000269|PubMed:12560483, ECO:0000269|PubMed:18066052, ECO:0000269|PubMed:22901803

Chain	Residue	Details
A	THR11
E	THR11

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435

Chain	Residue	Details
A	ILE14
A	LYS56
E	ILE14
E	LYS56

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: Citrulline; alternate => ECO:0000269|PubMed:15345777, ECO:0000269|PubMed:16497732, ECO:0000269|PubMed:16567635

Chain	Residue	Details
A	ARG17
E	ARG17
G	LYS119

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:17194708

Chain	Residue	Details
A	LYS18
A	LYS64
E	LYS18
E	LYS64

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:17194708

Chain	Residue	Details
A	LYS23
E	LYS23
H	ARG86
H	ARG92

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: Citrulline => ECO:0000269|PubMed:16567635

Chain	Residue	Details
A	CYS26
E	CYS26
F	LYS91

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16185088, ECO:0000269|PubMed:16267050, ECO:0000269|PubMed:17194708, ECO:0000269|PubMed:7309716

Chain	Residue	Details
A	LYS27
A	LYS36
E	LYS27
E	LYS36
F	LYS59
F	LYS79

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	MOD_RES: Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5 => ECO:0000269|PubMed:10464286, ECO:0000269|PubMed:11856369, ECO:0000269|PubMed:15681610, ECO:0000269|PubMed:15684425, ECO:0000269|PubMed:15851689, ECO:0000269|PubMed:16185088

Chain	Residue	Details
A	SER28
E	SER28

---

site_id	SWS_FT_FI18
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:15851689, ECO:0000269|PubMed:16185088

Chain	Residue	Details
A	SER31
E	SER31
H	LYS120

---

site_id	SWS_FT_FI19
Number of Residues	2
Details	MOD_RES: N6-methyllysine => ECO:0000250|UniProtKB:P68431

Chain	Residue	Details
A	LYS37
E	LYS37

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	MOD_RES: Phosphotyrosine => ECO:0000269|PubMed:19783980

Chain	Residue	Details
A	TYR41
E	TYR41

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:20850016

Chain	Residue	Details
A	SER57
E	SER57

---

site_id	SWS_FT_FI22
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_FI23
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016

Chain	Residue	Details
A	THR80
E	THR80

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
A	ARG86
E	ARG86

---

site_id	SWS_FT_FI25
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR107
E	THR107

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
A	THR115
E	THR115

---

site_id	SWS_FT_FI27
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_FI28
Number of Residues	2
Details	LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806

Chain	Residue	Details
A	LYS18
E	LYS18

---