Annotations: 6J2P

Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
D	Fungal_lectin	e6j2pD1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: Fungal_lectin	ECOD (v295.2)
C	Fungal_lectin	e6j2pC1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: Fungal_lectin	ECOD (v295.2)
B	Fungal_lectin	e6j2pB1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: Fungal_lectin	ECOD (v295.2)
A	Spp1_C3H_ZnF	e6j2pA2	A: alpha arrays	X: CCCH zinc finger	H: SSP1 C3H-type zinc finger	T: SSP1 C3H-type zinc finger	F: Spp1_C3H_ZnF	ECOD (v295.2)
A	PrgH	e6j2pA1	A: alpha arrays	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Family A G protein-coupled receptor-like	F: PrgH	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	COMPASS component SPP1	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular 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 regulation of nucleobase-containing compound metabolic 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 regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process subtelomeric heterochromatin formation negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression constitutive heterochromatin formation negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process sexual reproduction regulation of reproductive process reproductive process meiotic cell cycle process regulation of meiotic DNA double-strand break formation cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process meiotic cell cycle DNA metabolic process meiotic DNA double-strand break formation meiosis I cell cycle process regulation of DNA metabolic process	membrane-bounded organelle protein-containing complex Set1C/COMPASS complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membrane-bounded organelle protein-containing complex Set1C/COMPASS complex histone methyltransferase complex intracellular anatomical structure catalytic complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle methyltransferase complex nuclear lumen cytoplasm cytosol membraneless organelle intracellular membraneless organelle chromosome chromosome, telomeric region chromosomal region
E, F, G, H	Histone H3	protein heterodimerization activity protein binding binding protein dimerization activity structural molecule activity structural constituent of chromatin DNA binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding identical protein binding protein heterodimerization activity protein binding binding protein dimerization activity structural molecule activity structural constituent of chromatin DNA binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding identical protein binding oxidoreductase activity, acting on metal ions oxidoreductase activity oxidoreductase activity, acting on metal ions, NAD or NADP as acceptor cupric reductase (NADH) activity catalytic activity	inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis organelle assembly protein-containing complex organization chromosome organization inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis organelle assembly protein-containing complex organization chromosome organization membraneless organelle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly kinetochore assembly protein-containing complex assembly kinetochore organization cellular process cellular component organization or biogenesis aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy mitotic nuclear division mitotic metaphase chromosome alignment organelle fission sister chromatid segregation mitotic cell cycle metaphase chromosome alignment localization nuclear division mitotic cell cycle process chromosome localization organelle localization nuclear chromosome segregation mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process cellular response to stimulus global genome nucleotide-excision repair response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress macromolecule metabolic process DNA repair nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription rRNA 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 macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of biological process chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA 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	protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain cellular anatomical structure CENP-A containing nucleosome organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain cellular anatomical structure CENP-A containing nucleosome organelle membraneless organelle chromosome, centromeric region kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001965	Zinc finger, PHD-type	Domain
A, B, C, D	IPR037869	Spp1/CFP1	Family
A, B, C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR019787	Zinc finger, PHD-finger	Domain
A, B, C, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B, C, D	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
E, F, G, H	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
E, F, G, H	IPR000164	Histone H3/CENP-A	Family
E, F, G, H	IPR009072	Histone-fold	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H	M3L	Parent Component: LYS : AA0074 : N6,N6,N6-trimethyl-L-lysine MOD:00083

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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.