Annotations: 9LQP

Structure of transposase-activated RAG (RAG1 E962N) target capture complex with disordered U-shaped target DNA (TCC-UD)

External Resource: Annotation

Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	V(D)J recombination-activating protein 1	protein binding binding histone binding hydrolase activity catalytic activity sequence-specific DNA binding DNA binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity protein binding binding histone binding hydrolase activity catalytic activity sequence-specific DNA binding DNA binding nucleic acid binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin-protein transferase activity identical protein binding protein homodimerization activity protein dimerization activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 immune system development animal organ development gland development hematopoietic or lymphoid organ development multicellular organism development thymus development animal gross anatomical part developmental process system development response to stimulus immune response adaptive immune response regulation of defense response regulation of biological process behavioral fear response defense response regulation of fear response biological regulation multicellular organismal response to stress regulation of behavioral fear response regulation of behavior behavior behavioral defense response fear response regulation of response to stimulus regulation of response to stress response to stress regulation of multicellular organismal process protein autoubiquitination primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal multicellular organismal-level homeostasis leukocyte homeostasis T cell homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis regulation of leukocyte differentiation regulation of cellular process regulation of developmental process regulation of leukocyte activation regulation of cell activation regulation of cell differentiation regulation of cell development regulation of T cell differentiation T cell activation T cell differentiation regulation of immune system process regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of T cell activation regulation of hemopoiesis regulation of lymphocyte activation response to light stimulus system process learning learning or memory nervous system process visual learning visual behavior cognition associative learning response to radiation response to abiotic stimulus nucleobase-containing compound metabolic process DNA recombination DNA metabolic process nucleic acid metabolic process T cell differentiation in thymus regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process negative regulation of programmed cell death leukocyte apoptotic process regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of T cell apoptotic process lymphocyte apoptotic process negative regulation of apoptotic process negative regulation of leukocyte apoptotic process negative regulation of cellular process regulation of T cell apoptotic process T cell apoptotic process apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process immature B cell differentiation pre-B cell allelic exclusion pre-B cell differentiation regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of thymocyte apoptotic process thymocyte apoptotic process regulation of thymocyte apoptotic process positive regulation of T cell differentiation positive regulation of developmental process positive regulation of cell activation positive regulation of leukocyte activation positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process positive regulation of biological process positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of cell-cell adhesion positive regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation cellular component organization chromatin organization cellular component organization or biogenesis somatic cell DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors	protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex
B, D	Early growth response protein 1,V(D)J recombination-activating protein 2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity core promoter sequence-specific DNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding hemi-methylated DNA-binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity double-stranded methylated DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein binding histone acetyltransferase binding enzyme binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding anion binding phosphatidylinositol binding phosphatidylinositol-3,5-bisphosphate binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol-3,4-bisphosphate binding phosphatidylinositol-3,4,5-trisphosphate binding	regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process protein modification process positive regulation of cellular process regulation of biological process regulation of post-translational protein modification regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process positive regulation of macromolecule metabolic process protein metabolic process protein modification process positive regulation of cellular process regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process cellular process macromolecule metabolic process post-translational protein modification regulation of metabolic process ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process regulation of biosynthetic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process response to stimulus response to stress response to ischemia cellular response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death regulation of neuron apoptotic process positive regulation of hormone metabolic process regulation of hormone biosynthetic process regulation of hormone metabolic process regulation of hormone levels hormone metabolic process positive regulation of hormone biosynthetic process regulation of biological quality hormone biosynthetic process multicellular organismal process connective tissue development renal system development kidney vasculature development multicellular organism development renal system vasculature development anatomical structure development nephron development system development blood vessel development developmental process cell population proliferation animal organ development cell proliferation involved in kidney development glomerular mesangium development tissue development vasculature development circulatory system development glomerulus development glomerular mesangial cell proliferation glomerulus vasculature development kidney development animal gross anatomical part developmental process positive regulation of locomotion regulation of cell motility positive regulation of smooth muscle cell migration regulation of smooth muscle cell migration positive regulation of cell migration smooth muscle cell migration muscle cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of steroid biosynthetic process ketone metabolic process steroid metabolic process regulation of lipid metabolic process lipid biosynthetic process C21-steroid hormone metabolic process regulation of small molecule metabolic process progesterone metabolic process small molecule metabolic process steroid biosynthetic process steroid hormone biosynthetic process olefinic compound biosynthetic process small molecule biosynthetic process progesterone biosynthetic process regulation of ketone biosynthetic process regulation of steroid metabolic process C21-steroid hormone biosynthetic process regulation of progesterone biosynthetic process regulation of ketone metabolic process olefinic compound metabolic process regulation of lipid biosynthetic process ketone biosynthetic process lipid metabolic process skeletal muscle cell differentiation cellular developmental process skeletal muscle tissue development striated muscle tissue development muscle structure development skeletal muscle organ development cell differentiation muscle tissue development muscle organ development hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell activation immune system process T cell differentiation leukocyte differentiation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of miRNA transcription positive regulation of miRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process miRNA transcription regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of miRNA transcription circadian regulation of gene expression circadian rhythm positive regulation of gene expression via chromosomal CpG island demethylation positive regulation of gene expression, epigenetic cellular component organization transcription by RNA polymerase II chromatin organization chromatin remodeling cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation transcription initiation-coupled chromatin remodeling interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production positive regulation of multicellular organismal process positive regulation of cytokine production regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of chemokine production chemokine production positive regulation of chemokine production regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus behavior circadian behavior locomotory behavior rhythmic behavior locomotor rhythm cellular response to nitrogen compound response to heparin response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to heparin multicellular organismal-level homeostasis homeostatic process temperature homeostasis circadian temperature homeostasis negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of transcription by RNA polymerase II metanephric glomerulus vasculature development metanephric glomerulus development regulation of glomerular mesangial cell proliferation positive regulation of glomerular mesangial cell proliferation metanephros development metanephric glomerular mesangial cell proliferation involved in metanephros development metanephric nephron development regulation of metanephric glomerular mesangial cell proliferation positive regulation of cell proliferation involved in kidney development positive regulation of glomerular metanephric mesangial cell proliferation metanephric glomerular mesangium development cell proliferation involved in metanephros development response to peptide cellular response to interleukin-8 response to interleukin-8 response to cytokine cellular response to cytokine stimulus cellular response to BMP stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation cellular response to abiotic stimulus response to gamma radiation response to hexose response to monosaccharide response to carbohydrate response to glucose system process learning or memory long-term memory nervous system process cognition memory response to hormone response to peptide hormone response to insulin response to mycophenolic acid cellular response to mycophenolic acid cytokine-mediated signaling pathway cellular response to interleukin-1 interleukin-1-mediated signaling pathway response to interleukin-1 regulation of protein sumoylation peptidyl-lysine modification peptidyl-amino acid modification regulation of protein modification by small protein conjugation or removal protein sumoylation protein modification by small protein conjugation protein modification by small protein conjugation or removal B cell activation B cell proliferation leukocyte proliferation B cell homeostatic proliferation mononuclear cell proliferation lymphocyte proliferation B cell differentiation B cell lineage commitment cell fate commitment defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus DNA recombination DNA metabolic process T cell differentiation in thymus mature B cell differentiation B cell activation involved in immune response cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response mature B cell differentiation involved in immune response immune response immune effector process T cell lineage commitment regulation of growth regulation of developmental growth regulation of developmental process developmental growth positive regulation of organ growth growth organ growth positive regulation of developmental process positive regulation of growth regulation of organ growth positive regulation of developmental growth regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation negative regulation of T cell differentiation in thymus regulation of cell differentiation regulation of cell development negative regulation of cell adhesion negative regulation of T cell differentiation regulation of immune system process negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of T cell differentiation in thymus negative regulation of lymphocyte activation leukocyte cell-cell adhesion regulation of T cell differentiation cell adhesion cell-cell adhesion negative regulation of cell differentiation regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development negative regulation of developmental process regulation of cell adhesion regulation of T cell activation negative regulation of cell activation negative regulation of cell development negative regulation of immune system process regulation of hemopoiesis regulation of lymphocyte activation immature B cell differentiation pre-B cell allelic exclusion pre-B cell differentiation immune system development somatic cell DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex DNA recombinase complex protein-DNA complex
E [auth I]	Target DNA bottom strand	-	-	-
F [auth J]	Target DNA top strand	-	-	-
G [auth x]	23RSS bottom strand	-	-	-
H [auth M]	23RSS top strand	-	-	-
I [auth y]	12RSS bottom strand	-	-	-
J [auth L]	12RSS top strand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR024627	V(D)J recombination-activating protein 1	Family
A, C	IPR058552	V(D)J recombination-activating protein 1, DNA-binding domain	Domain
A, C	IPR019485	V(D)J recombination-activating protein 1, Zinc finger	Domain
A, C	IPR058553	V(D)J recombination-activating protein 1, pre-RNase H domain	Domain
A, C	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A, C	IPR023336	RAG nonamer-binding domain	Domain
A, C	IPR058557	V(D)J recombination-activating protein 1, C-terminal domain	Domain
A, C	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A, C	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, C	IPR058558	V(D)J recombination-activating protein 1, RING finger, HC subclass	Domain
A, C	IPR058556	V(D)J recombination-activating protein 1, ZnH2 domain	Domain
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR035714	RAG1 importin-binding	Domain
A, C	IPR058555	V(D)J recombination-activating protein 1, ZnC2 domain	Domain
A, C	IPR001841	Zinc finger, RING-type	Domain
A, C	IPR058554	V(D)J recombination-activating protein 1, RNase H domain	Domain
B, D	IPR013087	Zinc finger C2H2-type	Domain
B, D	IPR021849	Early growth response, N-terminal	Domain
B, D	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
B, D	IPR021839	Early growth response protein 1, C-terminal	Repeat
B, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B, D	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
B, D	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
B, D	IPR025162	Recombination activating protein 2, PHD domain	Domain
B, D	IPR004321	V-D-J recombination activating protein 2	Family

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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.

9LQP | pdb_00009lqp

Structure of transposase-activated RAG (RAG1 E962N) target capture complex with disordered U-shaped target DNA (TCC-UD)

External Resource: Annotation

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage