2YYR | pdb_00002yyr

Structural analysis of PHD domain of Pygopus complexed with trimethylated histone H3 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PHD	e2yyrA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)
B	PHD	e2yyrB1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
B	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	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
C [auth P]	H3K4Me3 peptide	-	-	-
A, B	Pygopus homolog 1	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process 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 cell differentiation anatomical structure development developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process 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 cell differentiation anatomical structure development germ cell development cellular process cellular component organization nucleus organization organelle organization cellular component organization or biogenesis spermatid nucleus differentiation cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication signal transduction Wnt signaling pathway hemopoiesis hematopoietic progenitor cell differentiation multicellular organism development multicellular organismal process animal organ development kidney development renal system development system development 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 transcription by RNA polymerase II 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 transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II 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 metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process localization protein localization to organelle macromolecule localization protein localization to nucleus intracellular protein localization	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
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR019787	Zinc finger, PHD-finger	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR052475	Wnt Signal Transduction Protein	Family
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth P]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083
A, B	MSE	Parent Component: MET RESID: AA0074

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.