6DBV

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs

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)
A	PF12940	e6dbvA3	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF12940	ECOD (1.6)
A	PF12940	e6dbvA1	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: PF12940	ECOD (1.6)
A	PF12940	e6dbvA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF12940	ECOD (1.6)
B	PF03089	e6dbvB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF03089	ECOD (1.6)
D	PF03089	e6dbvD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: PF03089	ECOD (1.6)
C	PF12940	e6dbvC3	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF12940	ECOD (1.6)
C	PF12940	e6dbvC1	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: PF12940	ECOD (1.6)
C	PF12940	e6dbvC2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF12940	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12940	Recombination-activation protein 1 (RAG1), recombinase (RAG1)	Recombination-activation protein 1 (RAG1), recombinase	-	Family
B, D	PF03089	Recombination activating protein 2 (RAG2)	Recombination activating protein 2	-	Repeat
C	PF12940	Recombination-activation protein 1 (RAG1), recombinase (RAG1)	Recombination-activation protein 1 (RAG1), recombinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Recombination activating gene 1 - MBP chimera	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein binding histone binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein binding histone binding sequence-specific DNA binding DNA binding organic cyclic compound 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 cation binding magnesium ion binding ion binding metal ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity transition metal ion binding zinc ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport organic substance transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to organic substance response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus 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 leukocyte differentiation immune response adaptive immune response cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex organization protein-containing complex assembly protein-DNA complex assembly cellular component organization or biogenesis T cell differentiation in thymus T cell activation T cell differentiation immune system development somatic cell DNA recombination DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process multicellular organism development organic substance metabolic process somatic diversification of immune receptors via germline recombination within a single locus metabolic process somatic diversification of immune receptors macromolecule metabolic process system development chromatin organization V(D)J recombination	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope DNA recombinase complex protein-DNA complex catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B, D	Recombination activating gene 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 protein-containing complex binding chromatin binding sequence-specific DNA binding DNA binding 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 protein-containing complex binding chromatin binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol-3,4-bisphosphate binding phosphatidylinositol-3,4,5-trisphosphate binding cation binding transition metal ion binding zinc ion binding metal ion binding methylated histone binding protein binding modification-dependent protein binding histone binding methylation-dependent protein binding	developmental process immune system development multicellular organism development multicellular organismal process immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular developmental process hemopoiesis B cell activation cell activation cell development developmental process immune system development multicellular organism development multicellular organismal process immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development 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 cellular process leukocyte differentiation gland development thymus development cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex organization protein-containing complex assembly protein-DNA complex assembly cellular component organization or biogenesis T cell activation T cell differentiation T cell differentiation in thymus immunoglobulin production cellular biosynthetic process somatic cell DNA recombination nucleobase-containing compound metabolic process V(D)J recombination somatic recombination of immunoglobulin gene segments organic substance metabolic process organic substance biosynthetic process somatic diversification of immune receptors production of molecular mediator of immune response DNA recombination cellular metabolic process primary metabolic process DNA metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process somatic diversification of immunoglobulins organic cyclic compound metabolic process immunoglobulin V(D)J recombination biosynthetic process somatic diversification of immune receptors via germline recombination within a single locus metabolic process macromolecule metabolic process chromatin organization	protein-containing complex DNA recombinase complex protein-DNA complex catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
C	Recombination activating gene 1 - MBP chimera	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein binding histone binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding protein binding histone binding sequence-specific DNA binding DNA binding organic cyclic compound 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 cation binding magnesium ion binding ion binding metal ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity transition metal ion binding zinc ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport organic substance transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to organic substance response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus 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 leukocyte differentiation immune response adaptive immune response cellular component organization cellular component biogenesis protein-DNA complex organization cellular component assembly protein-containing complex organization protein-containing complex assembly protein-DNA complex assembly cellular component organization or biogenesis T cell differentiation in thymus T cell activation T cell differentiation immune system development somatic cell DNA recombination DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process multicellular organism development organic substance metabolic process somatic diversification of immune receptors via germline recombination within a single locus metabolic process somatic diversification of immune receptors macromolecule metabolic process system development chromatin organization V(D)J recombination	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex cellular anatomical entity transporter complex ATP-binding cassette (ABC) transporter complex cell periphery transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope DNA recombinase complex protein-DNA complex catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
E	Forward strand of 12-RSS substrate DNA	-	-	-
F	Reverse strand of 12-RSS substrate DNA	-	-	-
G	Forward strand of 23-RSS substrate DNA	-	-	-
H	Reverse strand of 23-RSS substrate DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A	IPR024627	V(D)J recombination-activating protein 1	Family
A	IPR019485	V(D)J recombination-activating protein 1, Zinc finger	Domain
A	IPR023336	RAG nonamer-binding domain	Domain
A	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR035714	RAG1 importin-binding	Domain
A	IPR001841	Zinc finger, RING-type	Domain
B, D	IPR015915	Kelch-type beta propeller	Homologous Superfamily
B, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B, D	IPR011043	Galactose oxidase/kelch, 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
C	IPR006061	Solute-binding family 1, conserved site	Conserved Site
C	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
C	IPR006059	Bacterial-type extracellular solute-binding protein	Family
C	IPR024627	V(D)J recombination-activating protein 1	Family
C	IPR019485	V(D)J recombination-activating protein 1, Zinc finger	Domain
C	IPR023336	RAG nonamer-binding domain	Domain
C	IPR018957	Zinc finger, C3HC4 RING-type	Domain
C	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C	IPR035714	RAG1 importin-binding	Domain
C	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 R01GM133198.

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6DBV

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS substrate DNAs

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