4Z8L

Crystal structure of DCAF1/SIV-MND VPX/MND SAMHD1 NTD ternary complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	ANAPC4_WD40_8	e4z8lA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_8	ECOD (1.6)
D	ANAPC4_WD40_8	e4z8lD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: ANAPC4_WD40_8	ECOD (1.6)
B	VPR	e4z8lB1	A: alpha bundles	X: Viral accessory protein x (Vpx) / viral protein r (Vpr) (From Topology)	H: Viral accessory protein x (Vpx) / viral protein r (Vpr) (From Topology)	T: Viral accessory protein x (Vpx) / viral protein r (Vpr)	F: VPR	ECOD (1.6)
E	VPR	e4z8lE1	A: alpha bundles	X: Viral accessory protein x (Vpx) / viral protein r (Vpr) (From Topology)	H: Viral accessory protein x (Vpx) / viral protein r (Vpr) (From Topology)	T: Viral accessory protein x (Vpx) / viral protein r (Vpr)	F: VPR	ECOD (1.6)
C	SAM_1	e4z8lC1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: SAM_1	ECOD (1.6)
F	SAM_1	e4z8lF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: SAM_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	1.20.5.4730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E	1.20.5.4730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF07647	SAM domain (Sterile alpha motif) (SAM_2)	SAM domain (Sterile alpha motif)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Protein VPRBP	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H2AT120 kinase activity histone modifying activity histone H2A kinase activity catalytic activity histone kinase activity ubiquitin-like ligase-substrate adaptor activity enzyme-substrate adaptor activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding protein binding DNA-binding transcription factor binding nuclear estrogen receptor binding protein serine kinase activity	macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation multicellular organism development regulation of growth regulation of biological process biological regulation growth cell competition in a multicellular organism regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process catabolic process positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process macromolecule catabolic process positive regulation of catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process regulation of protein catabolic process protein ubiquitination protein modification by small protein conjugation protein modification by small protein conjugation or removal immune system development somatic cell DNA recombination DNA recombination DNA metabolic process V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors system development	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center organelle intracellular non-membrane-bounded organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm nucleoplasm cullin-RING ubiquitin ligase complex protein-containing complex ubiquitin ligase complex catalytic complex Cul4-RING E3 ubiquitin ligase complex transferase complex intracellular protein-containing complex
B, E	Vpx protein	cation binding ion binding binding metal ion binding small molecule binding	viral penetration into host nucleus intracellular transport of virus viral process viral life cycle transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction	host cellular component host cell cellular anatomical entity host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle virion component
C, F	SAM domain and HD domain-containing protein	catalytic activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding catalytic activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus cellular response to stimulus cellular response to stress DNA damage response cellular process DNA repair	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR016024	Armadillo-type fold	Homologous Superfamily
A, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, D	IPR011989	Armadillo-like helical	Homologous Superfamily
A, D	IPR033270	VPRBP/DCAF1 family	Family
A, D	IPR006594	LIS1 homology motif	Conserved Site
A, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, E	IPR053711	Lentiviral Vpx-associated factor	Homologous Superfamily
B, E	IPR000012	Retroviral VpR/VpX protein	Family
C, F	IPR003607	HD/PDEase domain	Domain
C, F	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
C, F	IPR050135	Deoxyguanosinetriphosphate triphosphohydrolase-like	Family
C, F	IPR001660	Sterile alpha motif domain	Domain
C, F	IPR006674	HD domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: Q9Y4B6	allergic rhinitis hepatocellular carcinoma ovarian cancer breast cancer medulloblastoma psoriasis cutaneous lupus erythematosus osteosarcoma tuberculosis

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.