2X4Y

Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.

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)
A	PWWP	e2x4yA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
C	PWWP	e2x4yC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
E	PWWP	e2x4yE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
G	PWWP	e2x4yG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
I	PWWP	e2x4yI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
K	PWWP	e2x4yK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
M	PWWP	e2x4yM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
O	PWWP	e2x4yO1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
K	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
M	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
O	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, C, E, G, I A, C, E, G, I, K, M, O	PF00855	PWWP domain (PWWP)	PWWP domain	The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic c ...	The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif [1]. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyses all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organising higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression [2].	Domain
B, D, F, H, J B, D, F, H, J, L, N, 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, C, E, G, I A, C, E, G, I, K, M, O	PEREGRIN	DNA binding binding organic cyclic compound binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity acetyltransferase activator activity molecular function regulator activity cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process regulation of biological process regulation of multicellular organismal development regulation of cellular process cellular developmental process regulation of developmental process hemopoiesis biological regulation cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation immune system process developmental process multicellular organismal process regulation of biological process regulation of multicellular organismal development regulation of cellular process cellular developmental process regulation of developmental process hemopoiesis biological regulation cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation immune system process anatomical structure development regulation of hemopoiesis cellular process regulation of immune system process regulation of multicellular organismal 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 cellular metabolic process 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 regulation of DNA-templated transcription macromolecule metabolic process 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 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 cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization chromatin remodeling cellular component organization or biogenesis	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 cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen MOZ/MORF histone acetyltransferase complex H3 histone acetyltransferase complex
B, D, F, H, J B, D, F, H, J, L, N, P	HISTONE H3.2	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	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001965	Zinc finger, PHD-type	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR013087	Zinc finger C2H2-type	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018359	Bromodomain, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001487	Bromodomain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR000313	PWWP domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR019787	Zinc finger, PHD-finger	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR042061	Peregrin, ePHD domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR019542	Enhancer of polycomb-like, N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR034732	Extended PHD (ePHD) domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR049583	Peregrin, PWWP domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O	IPR042008	BRPF1, PHD domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR009072	Histone-fold	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR007125	Histone H2A/H2B/H3	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: P55201	intellectual developmental disorder with dysmorphic facies and ptosis prostate cancer intellectual disability acute myeloid leukemia malignant mesothelioma psoriasis Prostatic Neoplasms
B, D, F, H, J B, D, F, H, J, L, N, P	Pharos: Q71DI3	idiopathic scoliosis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, L, N, 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 National Science Foundation (DBI-1832184), 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.