2V83

Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2v83a_	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2v83b2	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2v83b3	Artifacts	Tags	Tags	Tags	N-terminal Tags	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d2v83c2	Small proteins	FYVE/PHD zinc finger	FYVE/PHD zinc finger	PHD domain	automated matches	HOUSE MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d2v83c3	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)
B	SCOP2B Superfamily	FYVE/PHD zinc finger	8037379	3001459	SCOP2B (2022-06-29)
C	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	e2v83A1	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)
B	RAG2_PHD	e2v83B1	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)
C	RAG2_PHD	e2v83C1	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)
B	3.30.160.290	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Rag2 PHD finger	CATH (4.3.0)
C	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, B, C	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
D, E	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	VDJ 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 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 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 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	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 immune system process mononuclear cell proliferation 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 immune system process mononuclear cell proliferation 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 biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus T cell activation T cell differentiation nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance 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 regulation of leukocyte cell-cell adhesion negative regulation of lymphocyte differentiation 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 regulation of cell-cell adhesion negative regulation of cell differentiation 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 cellular biosynthetic process pre-B cell allelic exclusion pre-B cell differentiation organic substance biosynthetic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis 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	protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle protein-containing complex DNA recombinase complex protein-DNA complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
D, E	HISTONE H3	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR015915	Kelch-type beta propeller	Homologous Superfamily
A, B, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C	IPR011043	Galactose oxidase/kelch, beta-propeller	Homologous Superfamily
A, B, C	IPR025162	Recombination activating protein 2, PHD domain	Domain
A, B, C	IPR004321	V-D-J recombination activating protein 2	Family
D, E	IPR009072	Histone-fold	Homologous Superfamily
D, E	IPR007125	Histone H2A/H2B/H3	Domain
D, E	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, E	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D, E	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.