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	0006334	biological_process	nucleosome assembly
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	0031507	biological_process	heterochromatin formation
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	0006334	biological_process	nucleosome assembly
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	0031507	biological_process	heterochromatin formation
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	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"19783980","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"16267050","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"17194708","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29211711","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20850016","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"PubMed","id":"31542297","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"27436229","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	22
Details	Region: {"description":"M6 cassette","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	20
Details	Region: {"description":"Required for interaction with INCENP","evidences":[{"source":"PubMed","id":"12660166","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	1
Details	Modified residue: {"description":"N6-lactoyllysine","evidences":[{"source":"PubMed","id":"31645732","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---