2VPE | pdb_00002vpe

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex

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
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	YadA_stalk	e2vpeB01	A: a/b three-layered sandwiches	X: Caspase-like	H: Caspase-like	T: Caspase-like	F: YadA_stalk	ECOD (v294.1)
A	Leuk-A4-hydro_C	e2vpeA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Leuk-A4-hydro_C	ECOD (v294.1)
C	Leuk-A4-hydro_C	e2vpeC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Leuk-A4-hydro_C	ECOD (v294.1)

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)
C	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, 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
E [auth P], F [auth R]	HISTONE H3 TAIL	-	-	-
B, D	B-CELL CLL/LYMPHOMA 9 PROTEIN	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity beta-catenin binding protein binding binding	developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development cellular process myoblast 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 developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development cellular process myoblast 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 tissue regeneration skeletal muscle tissue regeneration developmental growth growth myotube differentiation involved in skeletal muscle regeneration muscle cell differentiation regeneration myotube differentiation striated muscle 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 multicellular organismal process somatic stem cell population maintenance maintenance of cell number stem cell population maintenance positive regulation of DNA-templated transcription positive regulation of biological process 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 positive regulation of cellular 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 animal organ development tissue development striated muscle tissue development skeletal muscle organ development muscle tissue development muscle organ development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm endomembrane system RNA polymerase II transcription regulator complex protein-containing complex nucleus nuclear protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm endomembrane system RNA polymerase II transcription regulator complex protein-containing complex nucleus nuclear protein-containing complex transcription regulator complex beta-catenin-TCF complex sarcoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, C	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 cellular component organization nucleus organization 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 cellular component organization nucleus organization organelle organization cell differentiation anatomical structure development germ cell development cellular process 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 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
B, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D	IPR015668	B Cell Lymphoma 9	Family
B, D	IPR024670	B-cell lymphoma 9, beta-catenin binding domain	Domain
A, C	IPR001965	Zinc finger, PHD-type	Domain
A, C	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C	IPR019787	Zinc finger, PHD-finger	Domain
A, C	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C	IPR052475	Wnt Signal Transduction Protein	Family
A, C	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: O00512	chromosome 1q21.1 deletion syndrome bipolar disorder lung cancer malignant mesothelioma ovarian neoplasm schizophrenia cancer lung carcinoma Malignant neoplasm of ovary primitive neuroectodermal tumor thrombocytopenia-absent radius syndrome major depressive disorder ovarian cancer
A, C	Pharos: Q9Y3Y4	astrocytic tumor lung carcinoma osteosarcoma atypical teratoid rhabdoid tumor malignant mesothelioma pilocytic astrocytoma large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth P], F [auth R]	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.