2JWO | pdb_00002jwo

A PHD finger motif in the C-terminus of RAG2 modulates recombination activity

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
A	d2jwoa1	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	V(D)J recombination-activating protein 2, Rag2	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2jwoa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FYVE/PHD zinc finger	8037379	3001459	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RAG2_PHD	e2jwoA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: RAG2_PHD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.160.290	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Rag2 PHD finger	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13341	RAG2 PHD domain (RAG2_PHD)	RAG2 PHD domain	This domain is found at the C-terminus of the RAG2 protein. The structure of this domain has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
A	IPR015915	Kelch-type beta-propeller	Homologous Superfamily
A	IPR025162	Recombination activating protein 2, PHD domain	Domain
A	IPR004321	V-D-J recombination activating protein 2	Family

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.