7V7C

CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000122	biological_process	negative regulation of transcription by RNA polymerase II
A	0000166	molecular_function	nucleotide binding
A	0001650	cellular_component	fibrillar center
A	0004674	molecular_function	protein serine/threonine kinase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005813	cellular_component	centrosome
A	0005856	cellular_component	cytoskeleton
A	0006325	biological_process	chromatin organization
A	0006338	biological_process	chromatin remodeling
A	0008180	cellular_component	COP9 signalosome
A	0016301	molecular_function	kinase activity
A	0016567	biological_process	protein ubiquitination
A	0016740	molecular_function	transferase activity
A	0030183	biological_process	B cell differentiation
A	0030331	molecular_function	nuclear estrogen receptor binding
A	0033151	biological_process	V(D)J recombination
A	0035212	biological_process	cell competition in a multicellular organism
A	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
A	0043687	biological_process	post-translational protein modification
A	0045732	biological_process	positive regulation of protein catabolic process
A	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
A	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
A	0106310	molecular_function	protein serine kinase activity
A	1990244	molecular_function	histone H2AT120 kinase activity
A	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
B	0000781	cellular_component	chromosome, telomeric region
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003684	molecular_function	damaged DNA binding
B	0005515	molecular_function	protein binding
B	0005615	cellular_component	extracellular space
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005730	cellular_component	nucleolus
B	0005737	cellular_component	cytoplasm
B	0006281	biological_process	DNA repair
B	0006289	biological_process	nucleotide-excision repair
B	0006511	biological_process	ubiquitin-dependent protein catabolic process
B	0006915	biological_process	apoptotic process
B	0006974	biological_process	DNA damage response
B	0007056	biological_process	spindle assembly involved in female meiosis
B	0010498	biological_process	proteasomal protein catabolic process
B	0016055	biological_process	Wnt signaling pathway
B	0016567	biological_process	protein ubiquitination
B	0019076	biological_process	viral release from host cell
B	0030674	molecular_function	protein-macromolecule adaptor activity
B	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
B	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
B	0032991	cellular_component	protein-containing complex
B	0034644	biological_process	cellular response to UV
B	0035234	biological_process	ectopic germ cell programmed cell death
B	0035861	cellular_component	site of double-strand break
B	0042752	biological_process	regulation of circadian rhythm
B	0043066	biological_process	negative regulation of apoptotic process
B	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
B	0044725	biological_process	epigenetic programming in the zygotic pronuclei
B	0044877	molecular_function	protein-containing complex binding
B	0045070	biological_process	positive regulation of viral genome replication
B	0045722	biological_process	positive regulation of gluconeogenesis
B	0045732	biological_process	positive regulation of protein catabolic process
B	0046726	biological_process	positive regulation by virus of viral protein levels in host cell
B	0048511	biological_process	rhythmic process
B	0051093	biological_process	negative regulation of developmental process
B	0051702	biological_process	biological process involved in interaction with symbiont
B	0051898	biological_process	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
B	0060337	biological_process	type I interferon-mediated signaling pathway
B	0070062	cellular_component	extracellular exosome
B	0070914	biological_process	UV-damage excision repair
B	0071987	molecular_function	WD40-repeat domain binding
B	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
B	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
B	0097602	molecular_function	cullin family protein binding
B	0160072	molecular_function	ubiquitin ligase complex scaffold activity
B	1901990	biological_process	regulation of mitotic cell cycle phase transition
B	2000242	biological_process	negative regulation of reproductive process
C	0005515	molecular_function	protein binding
C	0006351	biological_process	DNA-templated transcription
C	0006355	biological_process	regulation of DNA-templated transcription
C	0006811	biological_process	monoatomic ion transport
C	0019058	biological_process	viral life cycle
C	0034220	biological_process	monoatomic ion transmembrane transport
C	0039592	biological_process	symbiont-mediated arrest of host cell cycle during G2/M transition
C	0042025	cellular_component	host cell nucleus
C	0043655	cellular_component	host extracellular space
C	0043657	cellular_component	host cell
C	0044071	biological_process	symbiont-mediated perturbation of host cell cycle progression
C	0044423	cellular_component	virion component
C	0046718	biological_process	symbiont entry into host cell
C	0051260	biological_process	protein homooligomerization
C	0051701	biological_process	biological process involved in interaction with host
C	0052151	biological_process	symbiont-mediated activation of host apoptosis
C	0075732	biological_process	viral penetration into host nucleus
D	0004844	molecular_function	uracil DNA N-glycosylase activity
D	0006281	biological_process	DNA repair
D	0006284	biological_process	base-excision repair
D	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
E	0000122	biological_process	negative regulation of transcription by RNA polymerase II
E	0000166	molecular_function	nucleotide binding
E	0001650	cellular_component	fibrillar center
E	0004674	molecular_function	protein serine/threonine kinase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005813	cellular_component	centrosome
E	0005856	cellular_component	cytoskeleton
E	0006325	biological_process	chromatin organization
E	0006338	biological_process	chromatin remodeling
E	0008180	cellular_component	COP9 signalosome
E	0016301	molecular_function	kinase activity
E	0016567	biological_process	protein ubiquitination
E	0016740	molecular_function	transferase activity
E	0030183	biological_process	B cell differentiation
E	0030331	molecular_function	nuclear estrogen receptor binding
E	0033151	biological_process	V(D)J recombination
E	0035212	biological_process	cell competition in a multicellular organism
E	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
E	0043687	biological_process	post-translational protein modification
E	0045732	biological_process	positive regulation of protein catabolic process
E	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
E	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
E	0106310	molecular_function	protein serine kinase activity
E	1990244	molecular_function	histone H2AT120 kinase activity
E	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
F	0000781	cellular_component	chromosome, telomeric region
F	0003676	molecular_function	nucleic acid binding
F	0003677	molecular_function	DNA binding
F	0003684	molecular_function	damaged DNA binding
F	0005515	molecular_function	protein binding
F	0005615	cellular_component	extracellular space
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005730	cellular_component	nucleolus
F	0005737	cellular_component	cytoplasm
F	0006281	biological_process	DNA repair
F	0006289	biological_process	nucleotide-excision repair
F	0006511	biological_process	ubiquitin-dependent protein catabolic process
F	0006915	biological_process	apoptotic process
F	0006974	biological_process	DNA damage response
F	0007056	biological_process	spindle assembly involved in female meiosis
F	0010498	biological_process	proteasomal protein catabolic process
F	0016055	biological_process	Wnt signaling pathway
F	0016567	biological_process	protein ubiquitination
F	0019076	biological_process	viral release from host cell
F	0030674	molecular_function	protein-macromolecule adaptor activity
F	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
F	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
F	0032991	cellular_component	protein-containing complex
F	0034644	biological_process	cellular response to UV
F	0035234	biological_process	ectopic germ cell programmed cell death
F	0035861	cellular_component	site of double-strand break
F	0042752	biological_process	regulation of circadian rhythm
F	0043066	biological_process	negative regulation of apoptotic process
F	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
F	0044725	biological_process	epigenetic programming in the zygotic pronuclei
F	0044877	molecular_function	protein-containing complex binding
F	0045070	biological_process	positive regulation of viral genome replication
F	0045722	biological_process	positive regulation of gluconeogenesis
F	0045732	biological_process	positive regulation of protein catabolic process
F	0046726	biological_process	positive regulation by virus of viral protein levels in host cell
F	0048511	biological_process	rhythmic process
F	0051093	biological_process	negative regulation of developmental process
F	0051702	biological_process	biological process involved in interaction with symbiont
F	0051898	biological_process	negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
F	0060337	biological_process	type I interferon-mediated signaling pathway
F	0070062	cellular_component	extracellular exosome
F	0070914	biological_process	UV-damage excision repair
F	0071987	molecular_function	WD40-repeat domain binding
F	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
F	0097510	biological_process	base-excision repair, AP site formation via deaminated base removal
F	0097602	molecular_function	cullin family protein binding
F	0160072	molecular_function	ubiquitin ligase complex scaffold activity
F	1901990	biological_process	regulation of mitotic cell cycle phase transition
F	2000242	biological_process	negative regulation of reproductive process
G	0005515	molecular_function	protein binding
G	0006351	biological_process	DNA-templated transcription
G	0006355	biological_process	regulation of DNA-templated transcription
G	0006811	biological_process	monoatomic ion transport
G	0019058	biological_process	viral life cycle
G	0034220	biological_process	monoatomic ion transmembrane transport
G	0039592	biological_process	symbiont-mediated arrest of host cell cycle during G2/M transition
G	0042025	cellular_component	host cell nucleus
G	0043655	cellular_component	host extracellular space
G	0043657	cellular_component	host cell
G	0044071	biological_process	symbiont-mediated perturbation of host cell cycle progression
G	0044423	cellular_component	virion component
G	0046718	biological_process	symbiont entry into host cell
G	0051260	biological_process	protein homooligomerization
G	0051701	biological_process	biological process involved in interaction with host
G	0052151	biological_process	symbiont-mediated activation of host apoptosis
G	0075732	biological_process	viral penetration into host nucleus
H	0004844	molecular_function	uracil DNA N-glycosylase activity
H	0006281	biological_process	DNA repair
H	0006284	biological_process	base-excision repair
H	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds

Functional Information from PROSITE/UniProt

site_id	PS00130
Number of Residues	10
Details	U_DNA_GLYCOSYLASE Uracil-DNA glycosylase signature. KVVIlGQDPY

Chain	Residue	Details
D	LYS147-TYR156

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	62
Details	Domain: {"description":"Chromo"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	64
Details	Domain: {"description":"LisH","evidences":[{"source":"PROSITE-ProRule","id":"PRU00126","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	78
Details	Repeat: {"description":"WD 1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	82
Details	Repeat: {"description":"WD 2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	74
Details	Repeat: {"description":"WD 3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	64
Details	Repeat: {"description":"WD 4"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	84
Details	Repeat: {"description":"WD 5"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	398
Details	Region: {"description":"WD repeat-like region"}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	14
Details	Motif: {"description":"DWD box 1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	14
Details	Motif: {"description":"DWD box 2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1532
Details	Region: {"description":"Interaction with CDT1","evidences":[{"source":"PubMed","id":"15448697","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	686
Details	Region: {"description":"WD repeat beta-propeller A"}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	632
Details	Region: {"description":"WD repeat beta-propeller B; Interaction with CUL4A"}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q9ESW0","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 SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	82
Details	Region: {"description":"Homooligomerization","evidences":[{"source":"HAMAP-Rule","id":"MF_04080","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by host","evidences":[{"source":"HAMAP-Rule","id":"MF_04080","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_03166","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9724657","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1SSP","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8900285","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9724657","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1SSP","evidenceCode":"ECO:0000312"},{"source":"PDB","id":"4SKN","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8900285","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4SKN","evidenceCode":"ECO:0000312"}]}

Chain

Residue

Details

---