2XB1 | pdb_00002xb1

Crystal structure of the human Pygo2 PHD finger in complex with the B9L HD1 domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth C]	Cytochrome_CBB3	e2xb1C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Cytochrome_CBB3	ECOD (v294.1)
A	PPC	e2xb1A1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: PPC	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN	transcription coactivator activity transcription regulator activity transcription coregulator activity beta-catenin binding protein binding binding histone binding chromatin binding enzyme regulator activity histone acetyltransferase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding transcription coactivator activity transcription regulator activity transcription coregulator activity beta-catenin binding protein binding binding histone binding chromatin binding enzyme regulator activity histone acetyltransferase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication cellular process response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development myoblast differentiation canonical Wnt signaling pathway Wnt signaling pathway regulation of epithelial to mesenchymal transition multicellular organismal process regulation of developmental process positive regulation of biological process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process positive regulation of cellular process animal organ development tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process somatic stem cell population maintenance maintenance of cell number stem cell population maintenance anatomical structure morphogenesis cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process skeletal muscle cell differentiation skeletal muscle tissue development striated muscle tissue development skeletal muscle organ development muscle tissue development muscle organ development multicellular organism development head development central nervous system development brain development nervous system development system development spermatid development spermatid differentiation sexual reproduction spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cellular component organization nucleus organization organelle organization germ cell development cellular component organization or biogenesis spermatid nucleus differentiation sensory organ development eye development visual system development camera-type eye development sensory system development lens development in camera-type eye epithelium development cell population proliferation mammary gland development gland development regulation of mammary gland epithelial cell proliferation mammary gland epithelium development regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation mammary gland epithelial cell proliferation kidney development renal system development developmental growth growth roof of mouth development	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle beta-catenin-TCF complex membrane-enclosed lumen intracellular membraneless organelle RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle beta-catenin-TCF complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center membraneless organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B [auth C]	IPR015668	B Cell Lymphoma 9	Family
A, B [auth C]	IPR024670	B-cell lymphoma 9, beta-catenin binding domain	Domain
A, B [auth C]	IPR001965	Zinc finger, PHD-type	Domain
A, B [auth C]	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B [auth C]	IPR019787	Zinc finger, PHD-finger	Domain
A, B [auth C]	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B [auth C]	IPR052475	Wnt Signal Transduction Protein	Family
A, B [auth C]	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth C]	Pharos: Q9BRQ0	allergic rhinitis inflammatory bowel disease primary biliary cholangitis systemic sclerosis celiac disease neoplasm of mature B-cells rheumatoid arthritis vitiligo glioblastoma osteosarcoma Sjogren syndrome atrial fibrillation cutaneous melanoma ovarian carcinoma attention deficit hyperactivity disorder, inattentive type allergic rhinitis inflammatory bowel disease primary biliary cholangitis systemic sclerosis celiac disease neoplasm of mature B-cells rheumatoid arthritis vitiligo glioblastoma osteosarcoma Sjogren syndrome atrial fibrillation cutaneous melanoma ovarian carcinoma attention deficit hyperactivity disorder, inattentive type inflammatory bowel disease prostate carcinoma breast carcinoma osteosarcoma skin basal cell carcinoma

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.