3P8D | pdb_00003p8d

Crystal structure of the second Tudor domain of human PHF20 (homodimer form)

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		e3p8dB1	A: Glycosyl hydrolase domain-like	X: alpha/alpha toroid	H: alpha/alpha toroid	T: SH2_2	F:	ECOD (20:10:01)
A		e3p8dA1	A: Glycosyl hydrolase domain-like	X: alpha/alpha toroid	H: alpha/alpha toroid	T: SH2_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18115	DNA repair protein Crb2 Tudor domain (Tudor_3)	DNA repair protein Crb2 Tudor domain	This is the tudor domain found in DNA repair protein crb2. Structural and functional studies of Crb2 and its mammalian homologue 53BP1 indicate that the conserved tandem-Tudor domain of 53BP1 and Crb2 preferentially interacts with H4K20me2, though it ...	This is the tudor domain found in DNA repair protein crb2. Structural and functional studies of Crb2 and its mammalian homologue 53BP1 indicate that the conserved tandem-Tudor domain of 53BP1 and Crb2 preferentially interacts with H4K20me2, though it also binds to H4K20me1 [1]. Furthermore, despite low amino acid sequence similarity, Crb2 is structurally related to 53BP1 in having two tudor domains and a conserved dimethyllysine-binding pocket, and that, like 53BP1, it directly binds H4-K20me2 [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Medulloblastoma antigen MU-MB-50.72	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II cellular component organization chromatin organization cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex membrane-bounded organelle nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system organelle envelope nuclear envelope organelle membrane cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen histone methyltransferase complex nuclear protein-containing complex MLL1/2 complex MLL1 complex methyltransferase complex NSL complex H4 histone acetyltransferase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR022255	PHD finger protein 20, AT hook	Domain
A, B	IPR013087	Zinc finger C2H2-type	Domain
A, B	IPR002999	Tudor domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR041297	DNA repair protein Crb2, Tudor domain	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR043449	PHD finger protein 20-like	Family
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9BVI0	amyotrophic lateral sclerosis Crohn disease large cell medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor dermatomyositis malignant glioma skin carcinoma cerebrovascular disorder invasive ductal breast carcinoma medulloblastoma

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.