6B40 | pdb_00006b40

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

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
F [auth E]	RAG1_3rd	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: RAG1_3rd	ECOD (1.6)
F [auth E]	RAG1_2nd	e6b40E2	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	RAG1_3rd	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: RAG1_3rd	ECOD (1.6)
A	RAG1_2nd	e6b40A1	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth M], J [auth N]	RAG2L	-	-	-
D, I [auth H]	31TIR pre-nicked strand of flanking DNA	-	-	-
C, H [auth G]	31TIR pre-nicked strand of signal DNA	-	-	-
B, G [auth F]	31TIR intact strand	-	-	-
A, F [auth E]	RAG1L,RAG1L	protein binding binding histone binding identical protein binding protein homodimerization activity protein dimerization activity hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding transition metal ion binding zinc ion binding protein binding binding histone binding identical protein binding protein homodimerization activity protein dimerization activity hydrolase activity catalytic 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 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	cellular component 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 multicellular organism development cellular component 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 multicellular organism development V(D)J recombination 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 cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth M], J [auth N]	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
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]	IPR058552	V(D)J recombination-activating protein 1, DNA-binding domain	Domain
A, F [auth E]	IPR058553	V(D)J recombination-activating protein 1, pre-RNase H domain	Domain
A, F [auth E]	IPR058556	V(D)J recombination-activating protein 1, ZnH2 domain	Domain
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]	IPR058555	V(D)J recombination-activating protein 1, ZnC2 domain	Domain
A, F [auth E]	IPR023336	RAG nonamer-binding domain	Domain
A, F [auth E]	IPR001841	Zinc finger, RING-type	Domain
A, F [auth E]	IPR058557	V(D)J recombination-activating protein 1, C-terminal domain	Domain
A, F [auth E]	IPR058554	V(D)J recombination-activating protein 1, RNase H domain	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.