Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7XZX

Cryo-EM structure of the nucleosome in complex with p53 DNA-binding domain

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	0030527	molecular_function	structural constituent of chromatin
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	0046982	molecular_function	protein heterodimerization activity
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	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	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	0030527	molecular_function	structural constituent of chromatin
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	0046982	molecular_function	protein heterodimerization activity
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	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
K	0000976	molecular_function	transcription cis-regulatory region binding
K	0003677	molecular_function	DNA binding
K	0003700	molecular_function	DNA-binding transcription factor activity
K	0005634	cellular_component	nucleus
K	0006355	biological_process	regulation of DNA-templated transcription
K	0006915	biological_process	apoptotic process
L	0000976	molecular_function	transcription cis-regulatory region binding
L	0003677	molecular_function	DNA binding
L	0003700	molecular_function	DNA-binding transcription factor activity
L	0005634	cellular_component	nucleus
L	0006355	biological_process	regulation of DNA-templated transcription
L	0006915	biological_process	apoptotic process
M	0000976	molecular_function	transcription cis-regulatory region binding
M	0003677	molecular_function	DNA binding
M	0003700	molecular_function	DNA-binding transcription factor activity
M	0005634	cellular_component	nucleus
M	0006355	biological_process	regulation of DNA-templated transcription
M	0006915	biological_process	apoptotic process
N	0000976	molecular_function	transcription cis-regulatory region binding
N	0003677	molecular_function	DNA binding
N	0003700	molecular_function	DNA-binding transcription factor activity
N	0005634	cellular_component	nucleus
N	0006355	biological_process	regulation of DNA-templated transcription
N	0006915	biological_process	apoptotic process

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	PS00348
Number of Residues	13
Details	P53 p53 family signature. MCNSSCMGGMNRR

Chain	Residue	Details
K	MET237-ARG249

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

Chain	Residue	Details
D	ARG89-GLY111

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	760
Details	DNA_BIND: DNA_BIND => ECO:0000269\|PubMed:16793544, ECO:0000269\|PubMed:18996393, ECO:0000269\|PubMed:20364130

Chain	Residue	Details
K	THR102-LYS292
L	THR102-LYS292
M	THR102-LYS292
N	THR102-LYS292

site_id	SWS_FT_FI2
Number of Residues	16
Details	BINDING: BINDING => ECO:0000269\|PubMed:14534297, ECO:0000269\|PubMed:16793544, ECO:0000269\|PubMed:17015838, ECO:0000269\|PubMed:18650397, ECO:0000269\|PubMed:19515728, ECO:0000269\|PubMed:20142040, ECO:0000269\|PubMed:20364130

Chain	Residue	Details
K	CYS176
M	HIS179
M	CYS238
M	CYS242
N	CYS176
N	HIS179
N	CYS238
N	CYS242
K	HIS179
K	CYS238
K	CYS242
L	CYS176
L	HIS179
L	CYS238
L	CYS242
M	CYS176

site_id	SWS_FT_FI3
Number of Residues	4
Details	SITE: Interaction with DNA => ECO:0000269\|PubMed:16793544, ECO:0000269\|PubMed:18996393, ECO:0000269\|PubMed:20364130

Chain	Residue	Details
K	LYS120
H	LYS8
H	LYS12
H	LYS13
H	LYS17
H	LYS20
H	LYS40
H	LYS82
L	LYS120
M	LYS120
N	LYS120
D	LYS17
D	LYS20
D	LYS40
D	LYS82
H	LYS2

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:17189187, ECO:0000269\|PubMed:19854137, ECO:0000269\|PubMed:23431171

Chain	Residue	Details
K	LYS120
L	LYS120
M	LYS120
N	LYS120

site_id	SWS_FT_FI5
Number of Residues	8
Details	MOD_RES: Phosphoserine; by AURKB => ECO:0000269\|PubMed:20959462

Chain	Residue	Details
K	SER183
K	SER269
L	SER183
L	SER269
M	SER183
M	SER269
N	SER183
N	SER269

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphothreonine; by AURKB => ECO:0000269\|PubMed:20959462

Chain	Residue	Details
K	THR284
L	THR284
M	THR284
N	THR284
F	LYS12
F	LYS31
F	LYS77
F	LYS91

site_id	SWS_FT_FI7
Number of Residues	12
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:19536131

Chain	Residue	Details
K	LYS291
N	LYS291
N	LYS292
H	LYS21
K	LYS292
L	LYS291
L	LYS292
M	LYS291
M	LYS292

site_id	SWS_FT_FI8
Number of Residues	6
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269\|PubMed:22389435

Chain	Residue	Details
D	LYS31
D	LYS113
D	LYS117
H	LYS31
H	LYS113
H	LYS117

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250\|UniProtKB:Q64475

Chain	Residue	Details
D	GLU32
H	GLU32
C	LYS125
G	LYS118
G	LYS119
G	LYS125

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphoserine; by AMPK => ECO:0000250\|UniProtKB:Q64475

Chain	Residue	Details
D	SER33
H	SER33
E	LYS14
E	LYS56

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:16627869

Chain	Residue	Details
D	LYS43
D	LYS105
H	LYS43
H	LYS105

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

Chain	Residue	Details
D	LYS54
H	LYS54
E	LYS18
G	LYS119

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

Chain	Residue	Details
D	ARG76
H	ARG76

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

Chain	Residue	Details
D	ARG83
D	ARG89
H	ARG83
H	ARG89

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

Chain	Residue	Details
D	THR112
H	THR112
F	LYS91

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

Chain	Residue	Details
D	SER109
H	SER109
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 SUMO2); alternate => ECO:0000250\|UniProtKB:P58876

Chain	Residue	Details
D	LYS2
H	LYS2

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
A	LYS37
D	LYS117
H	LYS117

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
D	LYS17
H	LYS17

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
D	LYS31
H	LYS31

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

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