9B1E

Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000725	biological_process	recombinational repair
A	0000785	cellular_component	chromatin
A	0000812	cellular_component	Swr1 complex
A	0003677	molecular_function	DNA binding
A	0003678	molecular_function	DNA helicase activity
A	0004386	molecular_function	helicase activity
A	0005198	molecular_function	structural molecule activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005829	cellular_component	cytosol
A	0006325	biological_process	chromatin organization
A	0006338	biological_process	chromatin remodeling
A	0006355	biological_process	regulation of DNA-templated transcription
A	0016787	molecular_function	hydrolase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0031492	molecular_function	nucleosomal DNA binding
A	0042393	molecular_function	histone binding
A	0045815	biological_process	transcription initiation-coupled chromatin remodeling
A	0060090	molecular_function	molecular adaptor activity
A	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
B	0000785	cellular_component	chromatin
B	0000812	cellular_component	Swr1 complex
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0006325	biological_process	chromatin organization
B	0006338	biological_process	chromatin remodeling
B	0006355	biological_process	regulation of DNA-templated transcription
B	0042393	molecular_function	histone binding
C	0000785	cellular_component	chromatin
C	0000812	cellular_component	Swr1 complex
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0006325	biological_process	chromatin organization
C	0006338	biological_process	chromatin remodeling
C	0006355	biological_process	regulation of DNA-templated transcription
C	0031491	molecular_function	nucleosome binding
C	0034399	cellular_component	nuclear periphery
D	0000785	cellular_component	chromatin
D	0000812	cellular_component	Swr1 complex
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0006325	biological_process	chromatin organization
D	0006338	biological_process	chromatin remodeling
D	0006355	biological_process	regulation of DNA-templated transcription
D	0006623	biological_process	protein targeting to vacuole
D	0008270	molecular_function	zinc ion binding
D	0031491	molecular_function	nucleosome binding
D	0046872	molecular_function	metal ion binding
E	0000166	molecular_function	nucleotide binding
E	0000492	biological_process	box C/D snoRNP assembly
E	0000785	cellular_component	chromatin
E	0000812	cellular_component	Swr1 complex
E	0003678	molecular_function	DNA helicase activity
E	0004386	molecular_function	helicase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0006281	biological_process	DNA repair
E	0006325	biological_process	chromatin organization
E	0006338	biological_process	chromatin remodeling
E	0006355	biological_process	regulation of DNA-templated transcription
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0006974	biological_process	DNA damage response
E	0008094	molecular_function	ATP-dependent activity, acting on DNA
E	0008643	biological_process	carbohydrate transport
E	0015144	molecular_function	carbohydrate transmembrane transporter activity
E	0016787	molecular_function	hydrolase activity
E	0016887	molecular_function	ATP hydrolysis activity
E	0031011	cellular_component	Ino80 complex
E	0035267	cellular_component	NuA4 histone acetyltransferase complex
E	0043138	molecular_function	3'-5' DNA helicase activity
E	0043139	molecular_function	5'-3' DNA helicase activity
E	0050821	biological_process	protein stabilization
E	0055085	biological_process	transmembrane transport
E	0097255	cellular_component	R2TP complex
E	0110078	cellular_component	TTT Hsp90 cochaperone complex
F	0000166	molecular_function	nucleotide binding
F	0000492	biological_process	box C/D snoRNP assembly
F	0000785	cellular_component	chromatin
F	0000812	cellular_component	Swr1 complex
F	0003678	molecular_function	DNA helicase activity
F	0004386	molecular_function	helicase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0006281	biological_process	DNA repair
F	0006325	biological_process	chromatin organization
F	0006338	biological_process	chromatin remodeling
F	0006355	biological_process	regulation of DNA-templated transcription
F	0006357	biological_process	regulation of transcription by RNA polymerase II
F	0006364	biological_process	rRNA processing
F	0006974	biological_process	DNA damage response
F	0008094	molecular_function	ATP-dependent activity, acting on DNA
F	0016787	molecular_function	hydrolase activity
F	0016887	molecular_function	ATP hydrolysis activity
F	0031011	cellular_component	Ino80 complex
F	0035267	cellular_component	NuA4 histone acetyltransferase complex
F	0043138	molecular_function	3'-5' DNA helicase activity
F	0043139	molecular_function	5'-3' DNA helicase activity
F	0050821	biological_process	protein stabilization
F	0097255	cellular_component	R2TP complex
F	0110078	cellular_component	TTT Hsp90 cochaperone complex
G	0000166	molecular_function	nucleotide binding
G	0000492	biological_process	box C/D snoRNP assembly
G	0000785	cellular_component	chromatin
G	0000812	cellular_component	Swr1 complex
G	0003678	molecular_function	DNA helicase activity
G	0004386	molecular_function	helicase activity
G	0005515	molecular_function	protein binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0006281	biological_process	DNA repair
G	0006325	biological_process	chromatin organization
G	0006338	biological_process	chromatin remodeling
G	0006355	biological_process	regulation of DNA-templated transcription
G	0006357	biological_process	regulation of transcription by RNA polymerase II
G	0006974	biological_process	DNA damage response
G	0008094	molecular_function	ATP-dependent activity, acting on DNA
G	0008643	biological_process	carbohydrate transport
G	0015144	molecular_function	carbohydrate transmembrane transporter activity
G	0016787	molecular_function	hydrolase activity
G	0016887	molecular_function	ATP hydrolysis activity
G	0031011	cellular_component	Ino80 complex
G	0035267	cellular_component	NuA4 histone acetyltransferase complex
G	0043138	molecular_function	3'-5' DNA helicase activity
G	0043139	molecular_function	5'-3' DNA helicase activity
G	0050821	biological_process	protein stabilization
G	0055085	biological_process	transmembrane transport
G	0097255	cellular_component	R2TP complex
G	0110078	cellular_component	TTT Hsp90 cochaperone complex
H	0000166	molecular_function	nucleotide binding
H	0000492	biological_process	box C/D snoRNP assembly
H	0000785	cellular_component	chromatin
H	0000812	cellular_component	Swr1 complex
H	0003678	molecular_function	DNA helicase activity
H	0004386	molecular_function	helicase activity
H	0005515	molecular_function	protein binding
H	0005524	molecular_function	ATP binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0006281	biological_process	DNA repair
H	0006325	biological_process	chromatin organization
H	0006338	biological_process	chromatin remodeling
H	0006355	biological_process	regulation of DNA-templated transcription
H	0006357	biological_process	regulation of transcription by RNA polymerase II
H	0006364	biological_process	rRNA processing
H	0006974	biological_process	DNA damage response
H	0008094	molecular_function	ATP-dependent activity, acting on DNA
H	0016787	molecular_function	hydrolase activity
H	0016887	molecular_function	ATP hydrolysis activity
H	0031011	cellular_component	Ino80 complex
H	0035267	cellular_component	NuA4 histone acetyltransferase complex
H	0043138	molecular_function	3'-5' DNA helicase activity
H	0043139	molecular_function	5'-3' DNA helicase activity
H	0050821	biological_process	protein stabilization
H	0097255	cellular_component	R2TP complex
H	0110078	cellular_component	TTT Hsp90 cochaperone complex
I	0000166	molecular_function	nucleotide binding
I	0000492	biological_process	box C/D snoRNP assembly
I	0000785	cellular_component	chromatin
I	0000812	cellular_component	Swr1 complex
I	0003678	molecular_function	DNA helicase activity
I	0004386	molecular_function	helicase activity
I	0005515	molecular_function	protein binding
I	0005524	molecular_function	ATP binding
I	0005634	cellular_component	nucleus
I	0006281	biological_process	DNA repair
I	0006325	biological_process	chromatin organization
I	0006338	biological_process	chromatin remodeling
I	0006355	biological_process	regulation of DNA-templated transcription
I	0006357	biological_process	regulation of transcription by RNA polymerase II
I	0006974	biological_process	DNA damage response
I	0008094	molecular_function	ATP-dependent activity, acting on DNA
I	0008643	biological_process	carbohydrate transport
I	0015144	molecular_function	carbohydrate transmembrane transporter activity
I	0016787	molecular_function	hydrolase activity
I	0016887	molecular_function	ATP hydrolysis activity
I	0031011	cellular_component	Ino80 complex
I	0035267	cellular_component	NuA4 histone acetyltransferase complex
I	0043138	molecular_function	3'-5' DNA helicase activity
I	0043139	molecular_function	5'-3' DNA helicase activity
I	0050821	biological_process	protein stabilization
I	0055085	biological_process	transmembrane transport
I	0097255	cellular_component	R2TP complex
I	0110078	cellular_component	TTT Hsp90 cochaperone complex
J	0000166	molecular_function	nucleotide binding
J	0000492	biological_process	box C/D snoRNP assembly
J	0000785	cellular_component	chromatin
J	0000812	cellular_component	Swr1 complex
J	0003678	molecular_function	DNA helicase activity
J	0004386	molecular_function	helicase activity
J	0005515	molecular_function	protein binding
J	0005524	molecular_function	ATP binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0006281	biological_process	DNA repair
J	0006325	biological_process	chromatin organization
J	0006338	biological_process	chromatin remodeling
J	0006355	biological_process	regulation of DNA-templated transcription
J	0006357	biological_process	regulation of transcription by RNA polymerase II
J	0006364	biological_process	rRNA processing
J	0006974	biological_process	DNA damage response
J	0008094	molecular_function	ATP-dependent activity, acting on DNA
J	0016787	molecular_function	hydrolase activity
J	0016887	molecular_function	ATP hydrolysis activity
J	0031011	cellular_component	Ino80 complex
J	0035267	cellular_component	NuA4 histone acetyltransferase complex
J	0043138	molecular_function	3'-5' DNA helicase activity
J	0043139	molecular_function	5'-3' DNA helicase activity
J	0050821	biological_process	protein stabilization
J	0097255	cellular_component	R2TP complex
J	0110078	cellular_component	TTT Hsp90 cochaperone complex
K	0000785	cellular_component	chromatin
K	0000812	cellular_component	Swr1 complex
K	0005634	cellular_component	nucleus
K	0005739	cellular_component	mitochondrion
K	0006325	biological_process	chromatin organization
K	0006338	biological_process	chromatin remodeling
K	0006355	biological_process	regulation of DNA-templated transcription
K	0007029	biological_process	endoplasmic reticulum organization
K	0031492	molecular_function	nucleosomal DNA binding
K	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
Q	0000122	biological_process	negative regulation of transcription by RNA polymerase II
Q	0000786	cellular_component	nucleosome
Q	0003677	molecular_function	DNA binding
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005694	cellular_component	chromosome
Q	0006281	biological_process	DNA repair
Q	0006325	biological_process	chromatin organization
Q	0006974	biological_process	DNA damage response
Q	0030527	molecular_function	structural constituent of chromatin
Q	0031507	biological_process	heterochromatin formation
Q	0046982	molecular_function	protein heterodimerization activity
R	0000122	biological_process	negative regulation of transcription by RNA polymerase II
R	0000786	cellular_component	nucleosome
R	0003677	molecular_function	DNA binding
R	0005515	molecular_function	protein binding
R	0005634	cellular_component	nucleus
R	0005694	cellular_component	chromosome
R	0006301	biological_process	postreplication repair
R	0006325	biological_process	chromatin organization
R	0006355	biological_process	regulation of DNA-templated transcription
R	0030527	molecular_function	structural constituent of chromatin
R	0046982	molecular_function	protein heterodimerization activity
S	0000122	biological_process	negative regulation of transcription by RNA polymerase II
S	0000786	cellular_component	nucleosome
S	0003677	molecular_function	DNA binding
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005694	cellular_component	chromosome
S	0006281	biological_process	DNA repair
S	0006325	biological_process	chromatin organization
S	0006974	biological_process	DNA damage response
S	0030527	molecular_function	structural constituent of chromatin
S	0031507	biological_process	heterochromatin formation
S	0046982	molecular_function	protein heterodimerization activity
T	0000122	biological_process	negative regulation of transcription by RNA polymerase II
T	0000786	cellular_component	nucleosome
T	0003677	molecular_function	DNA binding
T	0005515	molecular_function	protein binding
T	0005634	cellular_component	nucleus
T	0005694	cellular_component	chromosome
T	0006301	biological_process	postreplication repair
T	0006325	biological_process	chromatin organization
T	0006355	biological_process	regulation of DNA-templated transcription
T	0030527	molecular_function	structural constituent of chromatin
T	0046982	molecular_function	protein heterodimerization activity
U	0000785	cellular_component	chromatin
U	0000786	cellular_component	nucleosome
U	0003677	molecular_function	DNA binding
U	0005515	molecular_function	protein binding
U	0005634	cellular_component	nucleus
U	0005694	cellular_component	chromosome
U	0005700	cellular_component	polytene chromosome
U	0006334	biological_process	nucleosome assembly
U	0030527	molecular_function	structural constituent of chromatin
U	0031492	molecular_function	nucleosomal DNA binding
U	0032991	cellular_component	protein-containing complex
U	0035059	cellular_component	RCAF complex
U	0046982	molecular_function	protein heterodimerization activity
V	0000786	cellular_component	nucleosome
V	0003677	molecular_function	DNA binding
V	0005634	cellular_component	nucleus
V	0005694	cellular_component	chromosome
V	0006325	biological_process	chromatin organization
V	0030527	molecular_function	structural constituent of chromatin
V	0046982	molecular_function	protein heterodimerization activity
W	0000785	cellular_component	chromatin
W	0000786	cellular_component	nucleosome
W	0003677	molecular_function	DNA binding
W	0005515	molecular_function	protein binding
W	0005634	cellular_component	nucleus
W	0005694	cellular_component	chromosome
W	0005700	cellular_component	polytene chromosome
W	0006334	biological_process	nucleosome assembly
W	0030527	molecular_function	structural constituent of chromatin
W	0031492	molecular_function	nucleosomal DNA binding
W	0032991	cellular_component	protein-containing complex
W	0035059	cellular_component	RCAF complex
W	0046982	molecular_function	protein heterodimerization activity
X	0000786	cellular_component	nucleosome
X	0003677	molecular_function	DNA binding
X	0005634	cellular_component	nucleus
X	0005694	cellular_component	chromosome
X	0006325	biological_process	chromatin organization
X	0030527	molecular_function	structural constituent of chromatin
X	0046982	molecular_function	protein heterodimerization activity

Functional Information from PROSITE/UniProt

site_id	PS00014
Number of Residues	4
Details	ER_TARGET Endoplasmic reticulum targeting sequence. SQEL

Chain	Residue	Details
Q	SER128-LEU131

---

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

Chain	Residue	Details
Q	ALA22-VAL28

---

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

Chain	Residue	Details
V	GLY14-HIS18

---

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
U	LYS14-LEU20

---

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

Chain	Residue	Details
R	ARG95-GLY117

---

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

Chain	Residue	Details
U	PRO66-ILE74

---

site_id	PS01037
Number of Residues	18
Details	SBP_BACTERIAL_1 Bacterial extracellular solute-binding proteins, family 1 signature. PIAvEalSLIYNkdlLpN

Chain	Residue	Details
E	PRO577-ASN594

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	165
Details	Domain: {"description":"Helicase ATP-binding","evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	153
Details	Domain: {"description":"Helicase C-terminal","evidences":[{"source":"PROSITE-ProRule","id":"PRU00542","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	Motif: {"description":"DEAH box"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00541","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	77
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	33
Details	Zinc finger: {"description":"HIT-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00453","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00453","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	42
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Site: {"description":"Not ubiquitinated","evidences":[{"source":"PubMed","id":"10642555","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2201907","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	7
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"source":"PubMed","id":"24352239","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	Modified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"PubMed","id":"19113941","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"10642555","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12535538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12535539","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14660635","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15280549","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16432255","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"14732680","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"PubMed","id":"22389435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---