2JMJ

NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 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	PF00628	e2jmjA1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF00628	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth P]	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	Protein YNG1	methylated histone binding protein binding binding modification-dependent protein binding histone binding methylation-dependent protein binding cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation positive regulation of nucleobase-containing compound metabolic process regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of cellular process DNA-templated transcription elongation positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis chromatin remodeling	protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex protein-DNA complex chromatin chromosome transferase complex cellular anatomical entity histone acetyltransferase complex acetyltransferase complex intracellular organelle organelle intracellular non-membrane-bounded organelle protein acetyltransferase complex intracellular protein-containing complex non-membrane-bounded organelle H3 histone acetyltransferase complex NuA3 histone acetyltransferase complex NuA3a histone acetyltransferase complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B [auth P]	Histone H3	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process 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 DNA-templated transcription regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process developmental process sexual sporulation resulting in formation of a cellular spore sexual reproduction reproductive process meiotic cell cycle developmental process involved in reproduction sporulation resulting in formation of a cellular spore anatomical structure morphogenesis sexual sporulation anatomical structure formation involved in morphogenesis anatomical structure development sporulation cell cycle cellular response to stimulus global genome nucleotide-excision repair response to stimulus DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle replication fork protection complex nuclear replication fork nuclear chromosome chromosome replication fork CENP-A containing chromatin protein-DNA complex nucleosome chromatin chromosomal region chromosome, centromeric core domain CENP-A containing nucleosome chromosome, centromeric region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR028651	ING family	Family
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B [auth P]	IPR009072	Histone-fold	Homologous Superfamily
B [auth P]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth P]	IPR000164	Histone H3/CENP-A	Family

Protein Modification Annotation

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

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 R01GM133198.