Annotations: 9DPI

Cryo-EM structure of SerRS dimer in complex with two SIRT2

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth F]	WD40	e9dpiF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)
A [auth D]	WD40	e9dpiD1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: WD40	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D [auth E]	PF02146	Sir2 family (SIR2)	Sir2 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], C [auth F]	Serine--tRNA ligase, cytoplasmic	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding tRNA binding adenyl ribonucleotide binding DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding tRNA 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 ligase activity, forming carbon-oxygen bonds aminoacyl-tRNA ligase activity selenocysteine-tRNA ligase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA catalytic activity ligase activity serine-tRNA ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity molecular adaptor activity enzyme binding	multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of vascular endothelial growth factor production negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation multicellular organismal process regulation of cellular process negative regulation of biological process negative regulation of vascular endothelial growth factor production negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression vascular endothelial growth factor production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process tRNA modification tRNA metabolic process RNA modification tRNA processing macromolecule modification RNA processing translation protein biosynthetic process cytoplasmic translation protein metabolic process tRNA C3-cytosine methylation macromolecule methylation methylation RNA methylation tRNA methylation selenocysteine incorporation regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of protein metabolic process translational readthrough regulation of translation translational elongation amino acid activation tRNA aminoacylation amino acid metabolic process tRNA aminoacylation for protein translation seryl-tRNA aminoacylation regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis animal gross anatomical part developmental process negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus intracellular membrane-bounded organelle
B [auth C], D [auth E]	NAD-dependent protein deacetylase sirtuin-2	histone deacetylase binding protein binding binding enzyme binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding histone deacetylase binding protein binding binding enzyme binding deacetylase activity protein lysine deacetylase activity catalytic activity, acting on a protein deacylase activity catalytic activity NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding NAD-dependent protein demyristoylase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity histone methacryllysine demethacrylase activity histone modifying activity pentosyltransferase activity NAD+ poly-ADP-ribosyltransferase activity glycosyltransferase activity tubulin deacetylase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds histone deacetylase activity chromatin binding ubiquitin binding ubiquitin-like protein binding histone deacetylase activity, NAD-dependent NAD-dependent protein lysine deacylase activity NAD-dependent protein lysine deacetylase activity histone acetyltransferase binding transcription factor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding metal ion binding NAD-dependent protein depalmitoylase activity histone H4K16 deacetylase activity, NAD-dependent histone H4K deacetylase activity histone benzoyllysine debenzoylase activity	regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding regulation of biological process regulation of cellular process phosphorylation phosphate-containing compound metabolic process regulation of phosphorylation cellular process metabolic process regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding regulation of biological process regulation of cellular process phosphorylation phosphate-containing compound metabolic process regulation of phosphorylation cellular process metabolic process regulation of metabolic process multicellular organismal process oligodendrocyte progenitor proliferation negative regulation of neural precursor cell proliferation cellular developmental process regulation of developmental process negative regulation of biological process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis regulation of cell development regulation of nervous system development neurogenesis multicellular organism development negative regulation of neurogenesis gliogenesis cell differentiation anatomical structure development negative regulation of cellular process regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation negative regulation of oligodendrocyte progenitor proliferation system development regulation of neural precursor cell proliferation developmental process regulation of multicellular organismal development negative regulation of cell population proliferation cell population proliferation negative regulation of developmental process nervous system development negative regulation of gliogenesis negative regulation of cell development regulation of cell population proliferation neural precursor cell proliferation negative regulation of multicellular organismal process animal gross anatomical part developmental process regulation of oligodendrocyte progenitor proliferation skeletal muscle cell differentiation skeletal muscle tissue development striated muscle tissue development muscle structure development skeletal muscle organ development regulation of skeletal muscle cell differentiation negative regulation of skeletal muscle cell differentiation muscle tissue development muscle organ development animal organ development tissue development negative regulation of satellite cell differentiation skeletal muscle satellite cell differentiation peptidyl-lysine deacetylation peptidyl-lysine modification primary metabolic process macromolecule deacylation protein deacetylation protein deacylation macromolecule modification peptidyl-amino acid modification protein metabolic process macromolecule metabolic process protein modification process regulation of cell cycle phase transition cell cycle phase transition exit from mitosis mitotic cell cycle cellular component organization regulation of mitotic cell cycle cell cycle cellular component organization or biogenesis regulation of cell cycle cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission regulation of mitotic cell cycle phase transition nuclear division organelle organization mitotic cell cycle process regulation of exit from mitosis mitotic cell cycle phase transition cell division peripheral nervous system axon ensheathment glial cell development axon ensheathment ensheathment of neurons myelination in peripheral nervous system Schwann cell differentiation peripheral nervous system development myelination Schwann cell development glial cell differentiation response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus response to redox state catabolic process autophagy process utilizing autophagic mechanism regulation of biosynthetic process epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process chromatin organization chromatin remodeling regulation of macromolecule biosynthetic process biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process positive regulation of biological process lipid biosynthetic process carboxylic acid biosynthetic process regulation of primary metabolic process positive regulation of fatty acid biosynthetic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process positive regulation of lipid metabolic process small molecule metabolic process positive regulation of cellular process positive regulation of fatty acid metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process regulation of ketone metabolic process positive regulation of lipid biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process lipid metabolic process positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteasome-mediated ubiquitin-dependent protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process positive regulation of ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process positive regulation of macromolecule metabolic process regulation of protein metabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process RNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of cell division regulation of cell division positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis apoptotic process programmed cell death response to oxidative stress cellular response to oxidative stress cellular response to chemical stress negative regulation of metabolic process reactive oxygen species metabolic process negative regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process subtelomeric heterochromatin formation cellular component biogenesis cellular component assembly negative regulation of macromolecule metabolic process heterochromatin formation heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic response to nutrient levels cellular response to caloric restriction response to caloric restriction negative regulation of catabolic process regulation of autophagy negative regulation of autophagy negative regulation of protein catabolic process negative regulation of protein metabolic process negative regulation of RNA biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II regulation of DNA-templated transcription negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process fat cell differentiation negative regulation of fat cell differentiation regulation of fat cell differentiation regulation of myelination regulation of protein modification process regulation of protein phosphorylation regulation of peptidyl-threonine phosphorylation negative regulation of phosphate metabolic process negative regulation of protein modification process peptidyl-threonine modification protein phosphorylation negative regulation of protein phosphorylation negative regulation of peptidyl-threonine phosphorylation negative regulation of phosphorylation peptidyl-threonine phosphorylation tubulin deacetylation mitotic nuclear membrane reassembly membrane biogenesis nuclear membrane reassembly endomembrane system organization membrane organization nuclear membrane organization membrane assembly nucleus organization mitotic nuclear membrane organization nuclear envelope organization response to epinephrine cellular response to epinephrine stimulus lipid catabolic process head development brain development substantia nigra development central nervous system development midbrain development neural nucleus development regulation of muscle tissue development negative regulation of muscle organ development regulation of striated muscle tissue development negative regulation of muscle tissue development regulation of muscle organ development negative regulation of striated muscle tissue development positive regulation of oocyte maturation sexual reproduction regulation of reproductive process reproductive process regulation of oocyte maturation cellular process involved in reproduction in multicellular organism positive regulation of cell maturation developmental process involved in reproduction female gamete generation gamete generation oocyte development positive regulation of developmental process positive regulation of cell differentiation cell maturation regulation of cell maturation positive regulation of reproductive process multicellular organismal reproductive process oogenesis positive regulation of cell development developmental maturation anatomical structure maturation germ cell development oocyte maturation oocyte differentiation meiotic cell cycle positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization meiotic cell cycle process positive regulation of cell cycle process meiotic nuclear division regulation of meiotic cell cycle positive regulation of nuclear division positive regulation of meiotic cell cycle regulation of organelle organization positive regulation of cell cycle regulation of meiotic nuclear division regulation of nuclear division positive regulation of meiotic nuclear division nucleolar chromatin organization rDNA heterochromatin formation nucleolus organization facultative heterochromatin formation regulation of chromosome segregation metaphase chromosome alignment localization chromosome localization organelle localization regulation of attachment of spindle microtubules to kinetochore chromosome segregation positive regulation of chromosome segregation attachment of spindle microtubules to kinetochore positive regulation of attachment of spindle microtubules to kinetochore nuclear chromosome segregation	axon cell projection cellular anatomical structure main axon juxtaparanode region of axon neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body perikaryon neuronal cell body cell-cell junction anchoring junction cell junction axon cell projection cellular anatomical structure main axon juxtaparanode region of axon neuron projection plasma membrane bounded cell projection somatodendritic compartment cell body perikaryon neuronal cell body cell-cell junction anchoring junction cell junction paranodal junction intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome chromatin heterochromatin perinuclear region of cytoplasm cytoskeleton spindle microtubule cytoskeleton chromosome, telomeric region chromosomal region polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex membrane-bounded organelle mitochondrion intracellular membrane-bounded organelle midbody nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen myelin sheath paranode region of axon centrosome microtubule organizing center centriole glial cell projection mitotic spindle growth cone distal axon site of polarized growth nucleoplasm protein-containing complex chromatin silencing complex nuclear protein-containing complex compact myelin Schmidt-Lanterman incisure lateral loop meiotic spindle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], C [auth F]	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A [auth D], C [auth F]	IPR002317	Serine-tRNA ligase, type1	Family
A [auth D], C [auth F]	IPR006195	Aminoacyl-tRNA synthetase, class II	Domain
A [auth D], C [auth F]	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)	Domain
A [auth D], C [auth F]	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm	Homologous Superfamily
A [auth D], C [auth F]	IPR033729	Serine-tRNA ligase catalytic core domain	Domain
A [auth D], C [auth F]	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily	Homologous Superfamily
A [auth D], C [auth F]	IPR015866	Serine-tRNA synthetase, type1, N-terminal	Domain
B [auth C], D [auth E]	IPR003000	Sirtuin family	Family
B [auth C], D [auth E]	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
B [auth C], D [auth E]	IPR017328	Sirtuin, class I	Family
B [auth C], D [auth E]	IPR026590	Sirtuin family, catalytic core domain	Domain
B [auth C], D [auth E]	IPR050134	NAD-dependent sirtuin protein deacylases	Family
B [auth C], D [auth E]	IPR026591	Sirtuin, catalytic core small domain superfamily	Homologous Superfamily

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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.

9DPI | pdb_00009dpi

Cryo-EM structure of SerRS dimer in complex with two SIRT2

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage