8Y3C

Cryo-EM structure of the overlapping di-nucleosome (closed form)

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
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	0010467	biological_process	gene expression
K	0016020	cellular_component	membrane
K	0032200	biological_process	telomere organization
K	0032991	cellular_component	protein-containing complex
K	0040029	biological_process	epigenetic regulation of gene expression
K	0045296	molecular_function	cadherin binding
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	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	0031507	biological_process	heterochromatin formation
M	0043505	cellular_component	CENP-A containing nucleosome
M	0061644	biological_process	protein localization to CENP-A containing chromatin
M	0070062	cellular_component	extracellular exosome
N	0000786	cellular_component	nucleosome
N	0001530	molecular_function	lipopolysaccharide binding
N	0002227	biological_process	innate immune response in mucosa
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	0005886	cellular_component	plasma membrane
N	0006325	biological_process	chromatin organization
N	0006334	biological_process	nucleosome assembly
N	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
N	0019731	biological_process	antibacterial humoral response
N	0031640	biological_process	killing of cells of another organism
N	0042742	biological_process	defense response to bacterium
N	0043505	cellular_component	CENP-A containing nucleosome
N	0050829	biological_process	defense response to Gram-negative bacterium
N	0050830	biological_process	defense response to Gram-positive bacterium
N	0061644	biological_process	protein localization to CENP-A containing chromatin
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	0010467	biological_process	gene expression
O	0016020	cellular_component	membrane
O	0032200	biological_process	telomere organization
O	0032991	cellular_component	protein-containing complex
O	0040029	biological_process	epigenetic regulation of gene expression
O	0045296	molecular_function	cadherin binding
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	0061644	biological_process	protein localization to CENP-A containing chromatin
P	0070062	cellular_component	extracellular exosome

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	3
Details	MOD_RES: N-acetylproline => ECO:0000250|UniProtKB:P23527

Chain	Residue	Details
D	PRO1
H	PRO1
N	PRO1
P	LYS16-LYS20

---

site_id	SWS_FT_FI2
Number of Residues	3
Details	MOD_RES: ADP-ribosyl glutamic acid => ECO:0000269|PubMed:27530147

Chain	Residue	Details
D	GLU2
H	GLU2
N	GLU2
P	SER1

---

site_id	SWS_FT_FI3
Number of Residues	24
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732

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

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	MOD_RES: ADP-ribosylserine => ECO:0000269|PubMed:34874266

Chain	Residue	Details
D	SER6
H	SER6
N	SER6
G	LYS95
M	LYS9
M	LYS95

---

site_id	SWS_FT_FI5
Number of Residues	3
Details	MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322

Chain	Residue	Details
D	LYS12
P	LYS8
P	LYS16
P	LYS44
H	LYS12
N	LYS12
F	LYS8
F	LYS16
F	LYS44
L	LYS8
L	LYS16
L	LYS44

---

site_id	SWS_FT_FI6
Number of Residues	3
Details	MOD_RES: Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711

Chain	Residue	Details
D	SER14
L	LYS31
L	LYS77
L	LYS91
P	LYS12
P	LYS31
P	LYS77
P	LYS91
H	SER14
N	SER14
B	LYS91
F	LYS12
F	LYS31
F	LYS77
F	LYS91
L	LYS12

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537

Chain	Residue	Details
D	LYS24
H	LYS24
N	LYS24
G	LYS75
M	LYS74
M	LYS75

---

site_id	SWS_FT_FI8
Number of Residues	9
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435

Chain	Residue	Details
D	LYS34
D	LYS116
D	LYS120
H	LYS34
H	LYS116
H	LYS120
N	LYS34
N	LYS116
N	LYS120

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475

Chain	Residue	Details
D	GLU35
H	GLU35
N	GLU35
G	LYS118
G	LYS119
G	LYS125
M	LYS118
M	LYS119
M	LYS125

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q64475

Chain	Residue	Details
D	SER36
H	SER36
N	SER36
P	LYS59
K	LYS14
K	LYS56
O	LYS14
O	LYS56

---

site_id	SWS_FT_FI11
Number of Residues	6
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869

Chain	Residue	Details
D	LYS46
D	LYS108
H	LYS46
H	LYS108
N	LYS46
N	LYS108

---

site_id	SWS_FT_FI12
Number of Residues	3
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537

Chain	Residue	Details
D	LYS57
H	LYS57
N	LYS57
G	LYS119
K	LYS18
M	LYS119
O	LYS18
O	LYS64

---

site_id	SWS_FT_FI13
Number of Residues	3
Details	MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
D	ARG79
H	ARG79
N	ARG79
P	TYR88

---

site_id	SWS_FT_FI14
Number of Residues	6
Details	MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
D	ARG86
D	ARG92
H	ARG86
H	ARG92
N	ARG86
N	ARG92

---

site_id	SWS_FT_FI15
Number of Residues	3
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729

Chain	Residue	Details
D	THR115
H	THR115
N	THR115
F	LYS91
L	LYS91
P	LYS91

---

site_id	SWS_FT_FI16
Number of Residues	3
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807

Chain	Residue	Details
D	SER112
P	LYS20
P	LYS59
P	LYS79
H	SER112
N	SER112
F	LYS20
F	LYS59
F	LYS79
L	LYS20
L	LYS59
L	LYS79

---

site_id	SWS_FT_FI17
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876

Chain	Residue	Details
D	LYS5
H	LYS5
N	LYS5
P	LYS31

---

site_id	SWS_FT_FI18
Number of Residues	6
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	LYS37
D	LYS120
K	LYS37
H	LYS120
N	LYS120

---

site_id	SWS_FT_FI19
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6

Chain	Residue	Details
D	LYS20
H	LYS20
N	LYS20
O	TYR41

---

site_id	SWS_FT_FI20
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816

Chain	Residue	Details
D	LYS34
H	LYS34
N	LYS34
O	SER57

---

site_id	SWS_FT_FI21
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711

Chain	Residue	Details
A	LYS79
E	LYS79
K	LYS79
O	LYS79

---

site_id	SWS_FT_FI22
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016

Chain	Residue	Details
A	THR80
E	THR80
K	THR80
O	THR80

---

site_id	SWS_FT_FI23
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
A	SER86
E	SER86
K	SER86
O	SER86

---

site_id	SWS_FT_FI24
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR107
E	THR107
K	THR107
O	THR107

---

site_id	SWS_FT_FI25
Number of Residues	4
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
A	LYS115
E	LYS115
K	LYS115
O	LYS115

---

site_id	SWS_FT_FI26
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229

Chain	Residue	Details
A	LYS122
E	LYS122
K	LYS122
O	LYS122

---

site_id	SWS_FT_FI27
Number of Residues	4
Details	LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806

Chain	Residue	Details
A	LYS18
E	LYS18
K	LYS18
O	LYS18

---