4CC9 | pdb_00004cc9

Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	VPR	e4cc9B1	A: alpha bundles	X: Alpha-beta plaits	H: Viral accessory protein x (Vpx) / viral protein r (Vpr)	T: Viral accessory protein x (Vpx) / viral protein r (Vpr)	F: VPR	ECOD (develop294)
A	Y_phosphatase	e4cc9A1	A: alpha bundles	X: dsRBD-like	H: Peptidyl-tRNA hydrolase domain-like	T: Peptidyl-tRNA hydrolase domain-like	F: Y_phosphatase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1	binding nucleic acid binding dGTP binding guanyl nucleotide binding deoxyribonucleotide binding nucleotide binding purine deoxyribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding guanyl deoxyribonucleotide binding heterocyclic compound binding carbohydrate derivative binding binding nucleic acid binding dGTP binding guanyl nucleotide binding deoxyribonucleotide binding nucleotide binding purine deoxyribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding guanyl deoxyribonucleotide binding heterocyclic compound binding carbohydrate derivative binding small molecule binding phosphoric ester hydrolase activity triphosphoric monoester hydrolase activity dGTPase activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity RNA binding GTP binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding ribonucleotide binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity deoxynucleoside triphosphate hydrolase activity cation binding transition metal ion binding zinc ion binding metal ion binding identical protein binding protein binding DNA binding single-stranded DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process immune response immune system process nucleoside phosphate metabolic process carbohydrate derivative catabolic process deoxyribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process immune response immune system process nucleoside phosphate metabolic process carbohydrate derivative catabolic process deoxyribonucleotide catabolic process catabolic process carbohydrate derivative metabolic process organophosphate catabolic process primary metabolic process nucleoside phosphate catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process deoxyribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process small molecule metabolic process phosphorus metabolic process nucleotide catabolic process regulation of cellular process regulation of type I interferon-mediated signaling pathway negative regulation of biological process response to cytokine regulation of signal transduction response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction regulation of biological process response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway regulation of response to stress negative regulation of cellular process innate immune response response to external biotic stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway biological regulation defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis immune system development developmental process production of molecular mediator of immune response multicellular organismal process immunoglobulin production somatic diversification of immune receptors via somatic mutation gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins multicellular organism development biosynthetic process anatomical structure development somatic diversification of immune receptors macromolecule metabolic process somatic hypermutation of immunoglobulin genes system development nucleoside triphosphate catabolic process purine nucleoside triphosphate catabolic process purine deoxyribonucleoside triphosphate metabolic process dGTP metabolic process deoxyribose phosphate catabolic process purine nucleotide metabolic process purine deoxyribonucleoside triphosphate catabolic process deoxyribonucleoside triphosphate metabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process purine deoxyribonucleotide catabolic process 2'-deoxyribonucleotide metabolic process purine-containing compound catabolic process deoxyribonucleoside triphosphate catabolic process purine-containing compound metabolic process purine deoxyribonucleotide metabolic process nucleoside triphosphate metabolic process dGTP catabolic process DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA metabolic process nucleic acid metabolic process DNA replication DNA strand resection involved in replication fork processing replication fork processing double-strand break repair DNA recombination recombinational repair double-strand break repair via homologous recombination DNA repair dATP metabolic process dATP catabolic process defense response to virus response to virus	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen site of double-strand break membraneless organelle site of DNA damage intracellular membraneless organelle chromosome tetraspanin-enriched microdomain
B	PROTEIN VPX	cation binding ion binding binding metal ion binding small molecule binding	symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral process viral life cycle	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle virion component
A	PROTEIN VPRBP	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 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 protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding 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	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 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 regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal proteasomal protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process multicellular organism development regulation of growth growth cell competition in a multicellular organism negative regulation of biological process RNA 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 negative regulation of metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic 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 negative regulation of RNA metabolic process 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	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nucleolus fibrillar center 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q9Y3Z3	Aicardi-Goutieres syndrome chilblain lupus Aicardi-Goutieres syndrome 5 chilblain lupus 2 mitochondrial DNA depletion syndrome, hepatocerebral form HIV infectious disease interstitial cystitis leukodystrophy lung carcinoma adenoma Mitochondrial Diseases Aicardi-Goutieres syndrome 2 non-small cell lung carcinoma astrocytic tumor ovarian cancer Aicardi-Goutieres syndrome chilblain lupus Aicardi-Goutieres syndrome 5 chilblain lupus 2 mitochondrial DNA depletion syndrome, hepatocerebral form HIV infectious disease interstitial cystitis leukodystrophy lung carcinoma adenoma Mitochondrial Diseases Aicardi-Goutieres syndrome 2 non-small cell lung carcinoma astrocytic tumor ovarian cancer pancreatic intraductal papillary-mucinous neoplasm pituitary cancer cutaneous lupus erythematosus subependymal giant cell astrocytoma Emery-Dreifuss muscular dystrophy gastric carcinoma IgA glomerulonephritis juvenile dermatomyositis limb-girdle muscular dystrophy malignant glioma oligodendroglioma B-cell chronic lymphocytic leukemia pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pseudo-TORCH syndrome tuberculosis glioblastoma intellectual disability large cell medulloblastoma lung cancer medulloblastoma Aicardi-Goutieres syndrome 1 myopathy osteosarcoma cerebrovascular disorder pancreatic intraductal papillary-mucinous carcinoma Crohn disease pilocytic astrocytoma Sjogren syndrome Duchenne muscular dystrophy ulcerative colitis facioscapulohumeral muscular dystrophy
A	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.