7U4D

CryoEM structure of CENP-N promoted nucleosome stacks with CENP-A and 601 DNA sequence

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000132	biological_process	establishment of mitotic spindle orientation
A	0000281	biological_process	mitotic cytokinesis
A	0000775	cellular_component	chromosome, centromeric region
A	0000779	cellular_component	condensed chromosome, centromeric region
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0003682	molecular_function	chromatin binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0005721	cellular_component	pericentric heterochromatin
A	0005829	cellular_component	cytosol
A	0030527	molecular_function	structural constituent of chromatin
A	0034080	biological_process	CENP-A containing chromatin assembly
A	0043229	cellular_component	intracellular organelle
A	0043505	cellular_component	CENP-A containing nucleosome
A	0046982	molecular_function	protein heterodimerization activity
A	0051301	biological_process	cell division
A	0051382	biological_process	kinetochore assembly
A	0061638	cellular_component	CENP-A containing chromatin
A	0061644	biological_process	protein localization to CENP-A containing chromatin
A	0071459	biological_process	protein localization to chromosome, centromeric region
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	0003674	molecular_function	molecular_function
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005694	cellular_component	chromosome
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	0046982	molecular_function	protein heterodimerization activity
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
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	0006334	biological_process	nucleosome assembly
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0042742	biological_process	defense response to bacterium
D	0042802	molecular_function	identical protein binding
D	0043229	cellular_component	intracellular organelle
D	0046982	molecular_function	protein heterodimerization activity
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
D	0070062	cellular_component	extracellular exosome
E	0000132	biological_process	establishment of mitotic spindle orientation
E	0000281	biological_process	mitotic cytokinesis
E	0000775	cellular_component	chromosome, centromeric region
E	0000779	cellular_component	condensed chromosome, centromeric region
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0003682	molecular_function	chromatin binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0005721	cellular_component	pericentric heterochromatin
E	0005829	cellular_component	cytosol
E	0030527	molecular_function	structural constituent of chromatin
E	0034080	biological_process	CENP-A containing chromatin assembly
E	0043229	cellular_component	intracellular organelle
E	0043505	cellular_component	CENP-A containing nucleosome
E	0046982	molecular_function	protein heterodimerization activity
E	0051301	biological_process	cell division
E	0051382	biological_process	kinetochore assembly
E	0061638	cellular_component	CENP-A containing chromatin
E	0061644	biological_process	protein localization to CENP-A containing chromatin
E	0071459	biological_process	protein localization to chromosome, centromeric region
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	0003674	molecular_function	molecular_function
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005694	cellular_component	chromosome
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	0046982	molecular_function	protein heterodimerization activity
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
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	0006334	biological_process	nucleosome assembly
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0042742	biological_process	defense response to bacterium
H	0042802	molecular_function	identical protein binding
H	0043229	cellular_component	intracellular organelle
H	0046982	molecular_function	protein heterodimerization activity
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
H	0070062	cellular_component	extracellular exosome
K	0007059	biological_process	chromosome segregation
K	0034080	biological_process	CENP-A containing chromatin assembly
L	0000132	biological_process	establishment of mitotic spindle orientation
L	0000281	biological_process	mitotic cytokinesis
L	0000775	cellular_component	chromosome, centromeric region
L	0000779	cellular_component	condensed chromosome, centromeric region
L	0000786	cellular_component	nucleosome
L	0003677	molecular_function	DNA binding
L	0003682	molecular_function	chromatin binding
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005694	cellular_component	chromosome
L	0005721	cellular_component	pericentric heterochromatin
L	0005829	cellular_component	cytosol
L	0030527	molecular_function	structural constituent of chromatin
L	0034080	biological_process	CENP-A containing chromatin assembly
L	0043229	cellular_component	intracellular organelle
L	0043505	cellular_component	CENP-A containing nucleosome
L	0046982	molecular_function	protein heterodimerization activity
L	0051301	biological_process	cell division
L	0051382	biological_process	kinetochore assembly
L	0061638	cellular_component	CENP-A containing chromatin
L	0061644	biological_process	protein localization to CENP-A containing chromatin
L	0071459	biological_process	protein localization to chromosome, centromeric region
M	0000781	cellular_component	chromosome, telomeric region
M	0000786	cellular_component	nucleosome
M	0003677	molecular_function	DNA binding
M	0003723	molecular_function	RNA binding
M	0005515	molecular_function	protein binding
M	0005576	cellular_component	extracellular region
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005694	cellular_component	chromosome
M	0006325	biological_process	chromatin organization
M	0006334	biological_process	nucleosome assembly
M	0016020	cellular_component	membrane
M	0030527	molecular_function	structural constituent of chromatin
M	0032200	biological_process	telomere organization
M	0032991	cellular_component	protein-containing complex
M	0043505	cellular_component	CENP-A containing nucleosome
M	0045653	biological_process	negative regulation of megakaryocyte differentiation
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	0003674	molecular_function	molecular_function
N	0003677	molecular_function	DNA binding
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005694	cellular_component	chromosome
N	0008285	biological_process	negative regulation of cell population proliferation
N	0030527	molecular_function	structural constituent of chromatin
N	0031492	molecular_function	nucleosomal DNA binding
N	0031507	biological_process	heterochromatin formation
N	0043229	cellular_component	intracellular organelle
N	0046982	molecular_function	protein heterodimerization activity
N	0070062	cellular_component	extracellular exosome
O	0000786	cellular_component	nucleosome
O	0002227	biological_process	innate immune response in mucosa
O	0003677	molecular_function	DNA binding
O	0005515	molecular_function	protein binding
O	0005615	cellular_component	extracellular space
O	0005634	cellular_component	nucleus
O	0005654	cellular_component	nucleoplasm
O	0005694	cellular_component	chromosome
O	0005829	cellular_component	cytosol
O	0006334	biological_process	nucleosome assembly
O	0019731	biological_process	antibacterial humoral response
O	0030527	molecular_function	structural constituent of chromatin
O	0042742	biological_process	defense response to bacterium
O	0042802	molecular_function	identical protein binding
O	0043229	cellular_component	intracellular organelle
O	0046982	molecular_function	protein heterodimerization activity
O	0050830	biological_process	defense response to Gram-positive bacterium
O	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
O	0070062	cellular_component	extracellular exosome
P	0000132	biological_process	establishment of mitotic spindle orientation
P	0000281	biological_process	mitotic cytokinesis
P	0000775	cellular_component	chromosome, centromeric region
P	0000779	cellular_component	condensed chromosome, centromeric region
P	0000786	cellular_component	nucleosome
P	0003677	molecular_function	DNA binding
P	0003682	molecular_function	chromatin binding
P	0005515	molecular_function	protein binding
P	0005634	cellular_component	nucleus
P	0005654	cellular_component	nucleoplasm
P	0005694	cellular_component	chromosome
P	0005721	cellular_component	pericentric heterochromatin
P	0005829	cellular_component	cytosol
P	0030527	molecular_function	structural constituent of chromatin
P	0034080	biological_process	CENP-A containing chromatin assembly
P	0043229	cellular_component	intracellular organelle
P	0043505	cellular_component	CENP-A containing nucleosome
P	0046982	molecular_function	protein heterodimerization activity
P	0051301	biological_process	cell division
P	0051382	biological_process	kinetochore assembly
P	0061638	cellular_component	CENP-A containing chromatin
P	0061644	biological_process	protein localization to CENP-A containing chromatin
P	0071459	biological_process	protein localization to chromosome, centromeric region
Q	0000781	cellular_component	chromosome, telomeric region
Q	0000786	cellular_component	nucleosome
Q	0003677	molecular_function	DNA binding
Q	0003723	molecular_function	RNA binding
Q	0005515	molecular_function	protein binding
Q	0005576	cellular_component	extracellular region
Q	0005634	cellular_component	nucleus
Q	0005654	cellular_component	nucleoplasm
Q	0005694	cellular_component	chromosome
Q	0006325	biological_process	chromatin organization
Q	0006334	biological_process	nucleosome assembly
Q	0016020	cellular_component	membrane
Q	0030527	molecular_function	structural constituent of chromatin
Q	0032200	biological_process	telomere organization
Q	0032991	cellular_component	protein-containing complex
Q	0043505	cellular_component	CENP-A containing nucleosome
Q	0045653	biological_process	negative regulation of megakaryocyte differentiation
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	0003674	molecular_function	molecular_function
R	0003677	molecular_function	DNA binding
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005654	cellular_component	nucleoplasm
R	0005694	cellular_component	chromosome
R	0008285	biological_process	negative regulation of cell population proliferation
R	0030527	molecular_function	structural constituent of chromatin
R	0031492	molecular_function	nucleosomal DNA binding
R	0031507	biological_process	heterochromatin formation
R	0043229	cellular_component	intracellular organelle
R	0046982	molecular_function	protein heterodimerization activity
R	0070062	cellular_component	extracellular exosome
S	0000786	cellular_component	nucleosome
S	0002227	biological_process	innate immune response in mucosa
S	0003677	molecular_function	DNA binding
S	0005515	molecular_function	protein binding
S	0005615	cellular_component	extracellular space
S	0005634	cellular_component	nucleus
S	0005654	cellular_component	nucleoplasm
S	0005694	cellular_component	chromosome
S	0005829	cellular_component	cytosol
S	0006334	biological_process	nucleosome assembly
S	0019731	biological_process	antibacterial humoral response
S	0030527	molecular_function	structural constituent of chromatin
S	0042742	biological_process	defense response to bacterium
S	0042802	molecular_function	identical protein binding
S	0043229	cellular_component	intracellular organelle
S	0046982	molecular_function	protein heterodimerization activity
S	0050830	biological_process	defense response to Gram-positive bacterium
S	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
S	0070062	cellular_component	extracellular exosome
V	0007059	biological_process	chromosome segregation
V	0034080	biological_process	CENP-A containing chromatin assembly

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
D	ARG92-GLY114

---

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

Chain	Residue	Details
B	GLY14-HIS18

---

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

Chain	Residue	Details
A	PRO66-ILE74

---

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

Chain	Residue	Details
C	ALA21-VAL27

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
K	SER226
V	SER226
O	PRO1
S	PRO1

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
K	SER235
V	SER235
O	GLU2
S	GLU2

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:18691976, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
H	LYS5
H	LYS11
H	LYS15
H	LYS16
H	LYS20
H	LYS23
H	LYS43
H	LYS85
O	LYS5
O	LYS11
O	LYS15
O	LYS16
O	LYS20
O	LYS23
O	LYS43
O	LYS85
S	LYS5
S	LYS11
S	LYS15
S	LYS16
S	LYS20
S	LYS23
S	LYS43
S	LYS85
K	SER282
V	SER282
D	LYS15
D	LYS16
D	LYS20
D	LYS23
D	LYS43
D	LYS85

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: ADP-ribosylserine => ECO:0000269|PubMed:34874266

Chain	Residue	Details
N	LYS9
N	LYS95
R	LYS9
R	LYS95
D	SER6
H	SER6
O	SER6
S	SER6

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322

Chain	Residue	Details
Q	LYS8
Q	LYS16
Q	LYS44
F	LYS16
F	LYS44
M	LYS8
M	LYS16
M	LYS44
D	LYS12
H	LYS12
O	LYS12
S	LYS12

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711

Chain	Residue	Details
Q	LYS12
Q	LYS31
Q	LYS77
Q	LYS91
D	SER14
H	SER14
O	SER14
S	SER14
F	LYS12
F	LYS31
F	LYS77
F	LYS91
M	LYS12
M	LYS31
M	LYS77
M	LYS91

---

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

Chain	Residue	Details
N	LYS74
N	LYS75
R	LYS74
R	LYS75
D	LYS24
H	LYS24
O	LYS24
S	LYS24

---

site_id	SWS_FT_FI8
Number of Residues	12
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435

Chain	Residue	Details
O	LYS120
S	LYS34
S	LYS116
S	LYS120
D	LYS34
D	LYS116
D	LYS120
H	LYS34
H	LYS116
H	LYS120
O	LYS34
O	LYS116

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475

Chain	Residue	Details
R	LYS118
R	LYS119
R	LYS125
G	LYS119
G	LYS125
N	LYS118
N	LYS119
N	LYS125
D	GLU35
H	GLU35
O	GLU35
S	GLU35

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q6ZWY9

Chain	Residue	Details
D	SER36
H	SER36
O	SER36
S	SER36

---

site_id	SWS_FT_FI11
Number of Residues	8
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869

Chain	Residue	Details
D	LYS46
D	LYS108
H	LYS46
H	LYS108
O	LYS46
O	LYS108
S	LYS46
S	LYS108

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537

Chain	Residue	Details
N	LYS119
R	LYS119
D	LYS57
H	LYS57
O	LYS57
S	LYS57

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
D	ARG79
H	ARG79
O	ARG79
S	ARG79

---

site_id	SWS_FT_FI14
Number of Residues	8
Details	MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
O	ARG86
O	ARG92
S	ARG86
S	ARG92
D	ARG86
D	ARG92
H	ARG86
H	ARG92

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729

Chain	Residue	Details
D	THR115
O	THR115
H	THR115
S	THR115
M	LYS91
Q	LYS91

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000269|PubMed:22121020

Chain	Residue	Details
Q	LYS20
Q	LYS59
Q	LYS79
F	LYS59
F	LYS79
M	LYS20
M	LYS59
M	LYS79
D	SER112
H	SER112
O	SER112
S	SER112

---

site_id	SWS_FT_FI17
Number of Residues	4
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
O	LYS5
S	LYS5

---

site_id	SWS_FT_FI18
Number of Residues	8
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, ECO:0000269|PubMed:22121020

Chain	Residue	Details
D	LYS120
H	LYS120
O	LYS120
S	LYS120

---

site_id	SWS_FT_FI19
Number of Residues	4
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
O	LYS20
S	LYS20

---

site_id	SWS_FT_FI20
Number of Residues	4
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
O	LYS34
S	LYS34

---