Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9B3P

The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome

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	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0030527	molecular_function	structural constituent of chromatin
B	0046982	molecular_function	protein heterodimerization activity
C	0000786	cellular_component	nucleosome
C	0000791	cellular_component	euchromatin
C	0000792	cellular_component	heterochromatin
C	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
C	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
C	0001740	cellular_component	Barr body
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	0030527	molecular_function	structural constituent of chromatin
C	0031490	molecular_function	chromatin DNA binding
C	0031492	molecular_function	nucleosomal DNA binding
C	0045944	biological_process	positive regulation of transcription by RNA polymerase II
C	0046982	molecular_function	protein heterodimerization activity
C	0071392	biological_process	cellular response to estradiol stimulus
D	0000786	cellular_component	nucleosome
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0030527	molecular_function	structural constituent of chromatin
D	0046982	molecular_function	protein heterodimerization activity
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	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0030527	molecular_function	structural constituent of chromatin
F	0046982	molecular_function	protein heterodimerization activity
G	0000786	cellular_component	nucleosome
G	0000791	cellular_component	euchromatin
G	0000792	cellular_component	heterochromatin
G	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
G	0000979	molecular_function	RNA polymerase II core promoter sequence-specific DNA binding
G	0001740	cellular_component	Barr body
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	0030527	molecular_function	structural constituent of chromatin
G	0031490	molecular_function	chromatin DNA binding
G	0031492	molecular_function	nucleosomal DNA binding
G	0045944	biological_process	positive regulation of transcription by RNA polymerase II
G	0046982	molecular_function	protein heterodimerization activity
G	0071392	biological_process	cellular response to estradiol stimulus
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0030527	molecular_function	structural constituent of chromatin
H	0046982	molecular_function	protein heterodimerization activity

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	ALA23-VAL29

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	8
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P0C1H4

Chain	Residue	Details
D	LYS5
D	LYS12
D	LYS15
D	LYS20
H	LYS5
H	LYS12
H	LYS15
H	LYS20

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:12757711

Chain	Residue	Details
D	SER14
H	SER14

site_id	SWS_FT_FI3
Number of Residues	2
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250\|UniProtKB:P62807

Chain	Residue	Details
D	SER112
H	SER112

site_id	SWS_FT_FI4
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250\|UniProtKB:P0C1H4

Chain	Residue	Details
D	LYS120
G	LYS115
H	LYS120

site_id	SWS_FT_FI5
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250\|UniProtKB:P0C0S5

Chain	Residue	Details
C	LYS121
B	LYS16
G	LYS121
B	LYS79
F	LYS8
F	LYS16
F	LYS44
F	LYS79

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	LYS12
B	LYS20
F	LYS12
F	LYS20

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	LYS31
B	LYS91
F	LYS31
F	LYS91

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: Phosphoserine; by PAK2 => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	SER47
F	SER47

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	TYR51
B	TYR88
F	TYR51
F	TYR88

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	LYS59
F	LYS59

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: N6-succinyllysine => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	LYS77
F	LYS77
E	LYS14
E	LYS56

site_id	SWS_FT_FI12
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
B	LYS31
F	LYS31

site_id	SWS_FT_FI13
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000250\|UniProtKB:P62805

Chain	Residue	Details
A	LYS18
B	LYS91
E	LYS18
F	LYS91

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

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

Chain	Residue	Details
A	ARG26
E	ARG26

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

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

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	SER86
E	SER86

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	LYS115
E	LYS115

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

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