6B40

BbRAGL-3'TIR synaptic complex with nicked DNA refined with C2 symmetry

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	e6b40A2	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	e6b40A1	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)
F [auth E]	PF12940	e6b40E1	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)
F [auth E]	PF12940	e6b40E2	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, F [auth E]	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, F [auth E]	RAG1L,RAG1L	protein binding binding histone binding identical protein binding protein homodimerization activity protein dimerization activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding protein binding binding histone binding identical protein binding protein homodimerization activity protein dimerization activity endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 ubiquitin-protein transferase activity	protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process cellular component organization or biogenesis immune system development developmental process multicellular organismal process somatic cell DNA recombination DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular process cellular component organization or biogenesis immune system development developmental process multicellular organismal process 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 V(D)J recombination organic substance metabolic process immune system process somatic diversification of immune receptors via germline recombination within a single locus anatomical structure development metabolic process somatic diversification of immune receptors macromolecule metabolic process system development	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity
B, G [auth F]	31TIR intact strand	-	-	-
C, H [auth G]	31TIR pre-nicked strand of signal DNA	-	-	-
D, I [auth H]	31TIR pre-nicked strand of flanking DNA	-	-	-
E [auth M], J [auth N]	RAG2L	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth E]	IPR024627	V(D)J recombination-activating protein 1	Family
A, F [auth E]	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, F [auth E]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, F [auth E]	IPR035714	RAG1 importin-binding	Domain
A, F [auth E]	IPR001841	Zinc finger, RING-type	Domain
E [auth M], J [auth N]	IPR015915	Kelch-type beta propeller	Homologous Superfamily

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.