4WWX | pdb_00004wwx

Crystal structure of the core RAG1/2 recombinase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth X]	d4wwxx_	Membrane and cell surface proteins and peptides	Helical insert domain of RAG1	Helical insert domain of RAG1	Recombination-activating protein RAG2-like	Recombination-activating protein RAG2	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d4wwxb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	DNA-binding domain of RAG1	Recombination-activating protein RAG1, nonamer-binding domain	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d4wwxb2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Ribonuclease H-like domain of RAG1	Recombination-activating protein RAG1	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d4wwxb3	Membrane and cell surface proteins and peptides	Helical insert domain of RAG1	Helical insert domain of RAG1	Helical insert domain of RAG1	Recombination-activating protein RAG1	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d4wwxb4	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth Y]	RAG2	e4wwxY1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: RAG2	ECOD (1.6)
B [auth X]	RAG2	e4wwxX1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: RAG2	ECOD (1.6)
C [auth E]	RAG1_1st	e4wwxE1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RAG1_1st	ECOD (1.6)
C [auth E]	RAG1_3rd	e4wwxE2	A: alpha bundles	X: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	H: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	T: V(D)J recombination-activating protein 1 helical bundle domain	F: RAG1_3rd	ECOD (1.6)
C [auth E]	RAG1_2nd	e4wwxE3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RAG1_2nd	ECOD (1.6)
A [auth B]	RAG1_1st	e4wwxB1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RAG1_1st	ECOD (1.6)
A [auth B]	RAG1_3rd	e4wwxB3	A: alpha bundles	X: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	H: V(D)J recombination-activating protein 1 helical bundle domain (From Topology)	T: V(D)J recombination-activating protein 1 helical bundle domain	F: RAG1_3rd	ECOD (1.6)
A [auth B]	RAG1_2nd	e4wwxB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RAG1_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	6.10.140.510	Special	Helix non-globular	Helix Hairpins		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth X], D [auth Y]	PF03089	Recombination activating protein 2 (RAG2)	Recombination activating protein 2	-	Repeat
A [auth B], C [auth E]	PF12940	Recombination-activation protein 1 (RAG1) nonamer-binding domain (RAG1)	Recombination-activation protein 1 (RAG1) nonamer-binding domain	This entry represents the N-terminal nonamer-binding domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 ...	This entry represents the N-terminal nonamer-binding domain of RAG1. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth X], D [auth Y]	V(D)J recombination-activating protein 2	binding phospholipid binding lipid binding phosphatidylinositol binding phosphatidylinositol-3,5-bisphosphate binding ion binding anion binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding small molecule binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity binding phospholipid binding lipid binding phosphatidylinositol binding phosphatidylinositol-3,5-bisphosphate binding ion binding anion binding phosphatidylinositol bisphosphate binding phosphatidylinositol phosphate binding small molecule binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding phosphatidylinositol-4,5-bisphosphate binding DNA binding nucleic acid binding phosphatidylinositol-3,4-bisphosphate binding phosphatidylinositol-3,4,5-trisphosphate binding cation binding transition metal ion binding zinc ion binding metal ion binding	multicellular organismal process cell population proliferation homeostatic process B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation B cell homeostatic proliferation leukocyte activation mononuclear cell proliferation immune system process lymphocyte proliferation cellular process multicellular organismal process cell population proliferation homeostatic process B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation B cell homeostatic proliferation leukocyte activation mononuclear cell proliferation immune system process lymphocyte proliferation cellular process developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation B cell lineage commitment cell fate commitment developmental growth growth organ growth defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus T cell activation T cell differentiation nucleobase-containing compound metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid 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 DN2 thymocyte differentiation regulation of biological process regulation of growth regulation of developmental growth regulation of developmental process positive regulation of organ growth biological regulation positive regulation of biological process positive regulation of developmental process positive regulation of growth regulation of organ growth positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of developmental growth regulation of leukocyte differentiation regulation of cellular process regulation of leukocyte activation negative regulation of biological process 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 multicellular organism development 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 cellular process 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 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 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 system development	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
A [auth B], C [auth E]	V(D)J recombination-activating protein 1	protein binding binding histone binding 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 catalytic activity protein binding binding histone binding 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 catalytic 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 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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth X], D [auth Y]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth X], D [auth Y]	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
B [auth X], D [auth Y]	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
B [auth X], D [auth Y]	IPR025162	Recombination activating protein 2, PHD domain	Domain
B [auth X], D [auth Y]	IPR004321	V-D-J recombination activating protein 2	Family
A [auth B], C [auth E]	IPR024627	V(D)J recombination-activating protein 1	Family
A [auth B], C [auth E]	IPR019485	V(D)J recombination-activating protein 1, Zinc finger	Domain
A [auth B], C [auth E]	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A [auth B], C [auth E]	IPR023336	RAG nonamer-binding domain	Domain
A [auth B], C [auth E]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A [auth B], C [auth E]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A [auth B], C [auth E]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth B], C [auth E]	IPR035714	RAG1 importin-binding	Domain
A [auth B], C [auth E]	IPR001841	Zinc finger, RING-type	Domain

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.