2X4Y | pdb_00002x4y

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)
O	PWWP	e2x4yO1	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)
K	PWWP	e2x4yK1	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)
G	PWWP	e2x4yG1	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)
C	PWWP	e2x4yC1	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)
O	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)
K	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)
G	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)
C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L, N, P	HISTONE H3.2	DNA binding binding nucleic acid binding chromatin binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 biosynthetic process protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process	cellular anatomical structure extracellular region 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 cellular anatomical structure extracellular region 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 intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, C, E, G, I A, C, E, G, I, K, M, O	PEREGRIN	DNA binding binding nucleic acid binding enzyme regulator activity enzyme activator activity molecular function activator activity acetyltransferase activator activity molecular function regulator activity cation binding transition metal ion binding zinc ion 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 regulation of developmental process cellular 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 regulation of developmental process cellular 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 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 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 metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process 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 transcription by RNA polymerase II regulation of transcription by RNA polymerase II cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	Core Histone H2A/H2B/H3 domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR000164	Histone H3/CENP-A	Family
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	IPR050701	Histone Modification Regulator	Family
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L, N, P	Pharos: Q71DI3	idiopathic scoliosis
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

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 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.