6DBI | pdb_00006dbi

Cryo-EM structure of RAG in complex with 12-RSS and 23-RSS nicked DNA intermediates

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)
D [auth B]	RAG2	e6dbiB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: RAG2	ECOD (1.6)
B [auth D]	RAG2	e6dbiD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 6-bladed	F: RAG2	ECOD (1.6)
C [auth A]	RAG1_1st	e6dbiA1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RAG1_1st	ECOD (1.6)
C [auth A]	RAG1_3rd	e6dbiA3	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 A]	RAG1_2nd	e6dbiA2	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 C]	RAG1_1st	e6dbiC2	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: RAG1_1st	ECOD (1.6)
A [auth C]	RAG1_3rd	e6dbiC1	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 C]	RAG1_2nd	e6dbiC3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D], D [auth B]	PF03089	Recombination activating protein 2 (RAG2)	Recombination activating protein 2	-	Repeat
A [auth C], C [auth A]	PF26105	Recombination-activation protein 1 (RAG1) C-terminal domain (RAG1_C)	Recombination-activation protein 1 (RAG1) C-terminal domain	This entry represents the C-terminal 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-bi ...	This entry represents the C-terminal 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
A [auth C], C [auth A]	PF26104	Recombination-activation protein 1 (RAG1) ZnH2 domain (RAG1_ZnH2)	Recombination-activation protein 1 (RAG1) ZnH2 domain	This entry represents the ZnH2 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 ...	This entry represents the ZnH2 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
A [auth C], C [auth A]	PF26025	Recombination-activation protein 1 (RAG1) pre-RNase H domain (RAG1_pre-RNase_H)	Recombination-activation protein 1 (RAG1) pre-RNase H domain	This entry represents the pre-RNase H 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-b ...	This entry represents the pre-RNase H 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
A [auth C], C [auth A]	PF26101	Recombination-activation protein 1 (RAG1) ZnC2 domain (RAG1_ZnC2)	Recombination-activation protein 1 (RAG1) ZnC2 domain	This entry represents the ZnC2 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 ...	This entry represents the ZnC2 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
A [auth C], C [auth A]	PF26024	Recombination-activation protein 1 (RAG1) DNA-binding domain (RAG1_DNA-bd)	Recombination-activation protein 1 (RAG1) DNA-binding domain	This entry represents the dimerisation and DNA-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]. RA ...	This entry represents the dimerisation and DNA-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
A [auth C], C [auth A]	PF26100	Recombination-activation protein 1 (RAG1) RNase H domain (RAG1_RNase_H)	Recombination-activation protein 1 (RAG1) RNase H domain	This entry represents the catalytic RNase H 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 ...	This entry represents the catalytic RNase H 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
I, J	Forward strand of coding flank	-	-	-
H	Forward strand of 23-RSS signal end	-	-	-
G	Reverse strand of 23-RSS	-	-	-
F	Reverse strand of 12-RSS	-	-	-
E	Forward strand of 12-RSS signal end	-	-	-
B [auth D], D [auth B]	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 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 sequence-specific DNA binding DNA 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	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 somatic cell DNA recombination nucleobase-containing compound metabolic process somatic recombination of immunoglobulin gene segments V(D)J recombination somatic diversification of immune receptors production of molecular mediator of immune response DNA recombination primary metabolic process DNA metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process somatic diversification of immune receptors via germline recombination within a single locus metabolic process macromolecule metabolic process	protein-containing complex DNA recombinase complex protein-DNA complex catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
A [auth C], C [auth A]	Recombination activating gene 1 - MBP chimera	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 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 catalytic activity, acting on a nucleic acid transition metal ion binding zinc ion binding transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding disaccharide binding carbohydrate binding maltose 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 response to stimulus 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 multicellular organism development somatic diversification of immune receptors via germline recombination within a single locus metabolic process somatic diversification of immune receptors macromolecule metabolic process system development regulation of cellular process immature B cell differentiation pre-B cell allelic exclusion pre-B cell differentiation regulation of biosynthetic process regulation of biological process biological regulation 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 chromatin organization V(D)J recombination cellular response to stimulus cellular response to stress DNA damage response response to stress cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization 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 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	protein-containing complex DNA recombinase complex protein-DNA complex catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle protein-containing complex DNA recombinase complex protein-DNA complex catalytic complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle ATPase dependent transmembrane transport complex plasma membrane protein complex membrane plasma membrane membrane protein complex 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth B]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth D], D [auth B]	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
B [auth D], D [auth B]	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
B [auth D], D [auth B]	IPR025162	Recombination activating protein 2, PHD domain	Domain
B [auth D], D [auth B]	IPR004321	V-D-J recombination activating protein 2	Family
A [auth C], C [auth A]	IPR024627	V(D)J recombination-activating protein 1	Family
A [auth C], C [auth A]	IPR058552	V(D)J recombination-activating protein 1, DNA-binding domain	Domain
A [auth C], C [auth A]	IPR019485	V(D)J recombination-activating protein 1, Zinc finger	Domain
A [auth C], C [auth A]	IPR058553	V(D)J recombination-activating protein 1, pre-RNase H domain	Domain
A [auth C], C [auth A]	IPR023336	RAG nonamer-binding domain	Domain
A [auth C], C [auth A]	IPR058557	V(D)J recombination-activating protein 1, C-terminal domain	Domain
A [auth C], C [auth A]	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A [auth C], C [auth A]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A [auth C], C [auth A]	IPR058558	V(D)J recombination-activating protein 1, RING finger, HC subclass	Domain
A [auth C], C [auth A]	IPR058556	V(D)J recombination-activating protein 1, ZnH2 domain	Domain
A [auth C], C [auth A]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A [auth C], C [auth A]	IPR035714	RAG1 importin-binding	Domain
A [auth C], C [auth A]	IPR058555	V(D)J recombination-activating protein 1, ZnC2 domain	Domain
A [auth C], C [auth A]	IPR001841	Zinc finger, RING-type	Domain
A [auth C], C [auth A]	IPR058554	V(D)J recombination-activating protein 1, RNase H domain	Domain
A [auth C], C [auth A]	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A [auth C], C [auth A]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A [auth C], C [auth A]	IPR006059	Bacterial-type extracellular solute-binding protein	Family