Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6K1J

Human nucleosome core particle with H2A.X variant

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	0043229	cellular_component	intracellular organelle
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	0000077	biological_process	DNA damage checkpoint signaling
C	0000724	biological_process	double-strand break repair via homologous recombination
C	0000781	cellular_component	chromosome, telomeric region
C	0000785	cellular_component	chromatin
C	0000786	cellular_component	nucleosome
C	0000794	cellular_component	condensed nuclear chromosome
C	0001673	cellular_component	male germ cell nucleus
C	0001741	cellular_component	XY body
C	0003677	molecular_function	DNA binding
C	0003684	molecular_function	damaged DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005657	cellular_component	replication fork
C	0005694	cellular_component	chromosome
C	0005813	cellular_component	centrosome
C	0006281	biological_process	DNA repair
C	0006302	biological_process	double-strand break repair
C	0006310	biological_process	DNA recombination
C	0006334	biological_process	nucleosome assembly
C	0006974	biological_process	DNA damage response
C	0007283	biological_process	spermatogenesis
C	0010212	biological_process	response to ionizing radiation
C	0016607	cellular_component	nuclear speck
C	0019899	molecular_function	enzyme binding
C	0021987	biological_process	cerebral cortex development
C	0030527	molecular_function	structural constituent of chromatin
C	0031492	molecular_function	nucleosomal DNA binding
C	0031507	biological_process	heterochromatin formation
C	0035861	cellular_component	site of double-strand break
C	0042393	molecular_function	histone binding
C	0043229	cellular_component	intracellular organelle
C	0045739	biological_process	positive regulation of DNA repair
C	0046982	molecular_function	protein heterodimerization activity
C	0051321	biological_process	meiotic cell cycle
C	0070062	cellular_component	extracellular exosome
C	0071480	biological_process	cellular response to gamma radiation
C	0090398	biological_process	cellular senescence
C	0090734	cellular_component	site of DNA damage
C	0140463	molecular_function	chromatin-protein adaptor activity
C	1990166	biological_process	protein localization to site of double-strand break
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	0043229	cellular_component	intracellular organelle
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	0043229	cellular_component	intracellular organelle
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	0000077	biological_process	DNA damage checkpoint signaling
G	0000724	biological_process	double-strand break repair via homologous recombination
G	0000781	cellular_component	chromosome, telomeric region
G	0000785	cellular_component	chromatin
G	0000786	cellular_component	nucleosome
G	0000794	cellular_component	condensed nuclear chromosome
G	0001673	cellular_component	male germ cell nucleus
G	0001741	cellular_component	XY body
G	0003677	molecular_function	DNA binding
G	0003684	molecular_function	damaged DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005657	cellular_component	replication fork
G	0005694	cellular_component	chromosome
G	0005813	cellular_component	centrosome
G	0006281	biological_process	DNA repair
G	0006302	biological_process	double-strand break repair
G	0006310	biological_process	DNA recombination
G	0006334	biological_process	nucleosome assembly
G	0006974	biological_process	DNA damage response
G	0007283	biological_process	spermatogenesis
G	0010212	biological_process	response to ionizing radiation
G	0016607	cellular_component	nuclear speck
G	0019899	molecular_function	enzyme binding
G	0021987	biological_process	cerebral cortex development
G	0030527	molecular_function	structural constituent of chromatin
G	0031492	molecular_function	nucleosomal DNA binding
G	0031507	biological_process	heterochromatin formation
G	0035861	cellular_component	site of double-strand break
G	0042393	molecular_function	histone binding
G	0043229	cellular_component	intracellular organelle
G	0045739	biological_process	positive regulation of DNA repair
G	0046982	molecular_function	protein heterodimerization activity
G	0051321	biological_process	meiotic cell cycle
G	0070062	cellular_component	extracellular exosome
G	0071480	biological_process	cellular response to gamma radiation
G	0090398	biological_process	cellular senescence
G	0090734	cellular_component	site of DNA damage
G	0140463	molecular_function	chromatin-protein adaptor activity
G	1990166	biological_process	protein localization to site of double-strand break
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	0043229	cellular_component	intracellular organelle
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 PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue CL C 201

Chain	Residue
C	GLY44
C	ALA45
C	GLY46
C	ALA47
D	THR87
D	SER88

site_id	AC2
Number of Residues	6
Details	binding site for residue MN D 201

Chain	Residue
E	HOH205
E	HOH206
F	HOH202
D	VAL45
E	ASP77
E	HOH204

site_id	AC3
Number of Residues	5
Details	binding site for residue CL H 201

Chain	Residue
G	GLY44
G	GLY46
H	THR87
H	SER88
I	DT38

site_id	AC4
Number of Residues	2
Details	binding site for residue MN I 101

Chain	Residue
I	DG-34
I	DG-33

site_id	AC5
Number of Residues	1
Details	binding site for residue MN I 103

Chain	Residue
I	DG47

site_id	AC6
Number of Residues	1
Details	binding site for residue MN I 104

Chain	Residue
I	DG60

site_id	AC7
Number of Residues	1
Details	binding site for residue MN J 101

Chain	Residue
J	DG60

site_id	AC8
Number of Residues	1
Details	binding site for residue MN J 102

Chain	Residue
J	DG47

site_id	AC9
Number of Residues	1
Details	binding site for residue MN J 103

Chain	Residue
J	DG26

site_id	AD1
Number of Residues	2
Details	binding site for residue MN J 104

Chain	Residue
I	DG-5
J	DG4

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	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	2
Details	MOD_RES: N-acetylproline => ECO:0000250\|UniProtKB:P23527

Chain	Residue	Details
D	PRO-2
H	PRO-2
G	SER1
G	SER121

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: ADP-ribosyl glutamic acid => ECO:0000269\|PubMed:27530147

Chain	Residue	Details
D	GLU-1
H	GLU-1

site_id	SWS_FT_FI3
Number of Residues	16
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000269\|PubMed:31645732

Chain	Residue	Details
D	LYS2
H	LYS8
H	LYS12
H	LYS13
H	LYS17
H	LYS20
H	LYS40
H	LYS82
D	LYS8
D	LYS12
D	LYS13
D	LYS17
D	LYS20
D	LYS40
D	LYS82
H	LYS2

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: ADP-ribosylserine => ECO:0000269\|PubMed:34874266

Chain	Residue	Details
D	SER3
H	SER3

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: N6-crotonyllysine; alternate => ECO:0000269\|PubMed:21925322

Chain	Residue	Details
D	LYS9
H	LYS9
B	LYS44
F	LYS8
F	LYS16
F	LYS44

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: Phosphoserine; by STK4/MST1 => ECO:0000269\|PubMed:12757711

Chain	Residue	Details
D	SER11
H	SER11
B	LYS77
B	LYS91
F	LYS12
F	LYS31
F	LYS77
F	LYS91

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

Chain	Residue	Details
D	LYS21
H	LYS21
G	LYS13
G	LYS15

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

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
E	LYS64

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)
		EDMap 2fo-fc (MTZ)