4N4I | pdb_00004n4i

Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.3K36me3

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	e4n4iA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
A	Bromodomain	e4n4iA2	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
A	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	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
A	PF00439	Bromodomain (Bromodomain)	Bromodomain	Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Peptide from Histone H3.3	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process cellular developmental process ossification cell differentiation osteoblast differentiation cell population proliferation negative regulation of biological process cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process pericentric heterochromatin formation regulation of gene expression negative regulation of gene expression constitutive heterochromatin formation biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process sexual reproduction fertilization single fertilization multi-multicellular organism process female pregnancy embryo implantation multi-organism reproductive process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental maturation female gamete generation gamete generation oocyte development anatomical structure maturation germ cell development oocyte maturation oocyte differentiation cell maturation protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization protein-containing complex assembly nucleosome assembly nucleosome organization spermatid development spermatid differentiation spermatogenesis male gamete generation negative regulation of cellular component organization regulation of chromosome condensation chromosome organization regulation of chromosome organization regulation of organelle organization negative regulation of chromosome condensation organelle organization negative regulation of chromosome organization negative regulation of organelle organization chromosome condensation subtelomeric heterochromatin formation telomere organization muscle structure development muscle cell differentiation nucleus organization multicellular organism growth developmental growth	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure intracellular membraneless organelle chromosome extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle membraneless organelle inner kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome protein-DNA complex nucleosome chromatin sex chromosome nucleus membrane-enclosed lumen nuclear chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen Barr body nuclear lumen X chromosome nucleoplasm chromosome, telomeric region
A	Zinc finger MYND domain-containing protein 11	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding double-stranded DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding double-stranded DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K36me3 reader activity	cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process transcription elongation by RNA polymerase II RNA metabolic process regulation of primary metabolic 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II 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 DNA-templated transcription elongation biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of JNK cascade JNK cascade regulation of JNK cascade regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway cell surface receptor signaling pathway negative regulation of programmed cell death regulation of apoptotic process cell death regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway biological process involved in interspecies interaction between organisms defense response to virus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus	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 membraneless organelle intracellular membraneless organelle 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 membraneless organelle intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B	IPR000164	Histone H3/CENP-A	Family
B	IPR009072	Histone-fold	Homologous Superfamily
A	IPR047269	Zinc finger MYND domain-containing protein 11	Family
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR057053	ZMYND11/ZMYD8, MYND zinc finger	Domain
A	IPR001487	Bromodomain	Domain
A	IPR000313	PWWP domain	Domain
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR047268	Zinc finger MYND domain-containing protein 11, PWWP domain	Domain
A	IPR048589	SAM domain-containing protein 1-like, WH domain	Domain
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR057054	ZMYND11, coiled-coil	Domain
A	IPR002893	Zinc finger, MYND-type	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR036427	Bromodomain-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P84243	malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer astrocytoma (excluding glioblastoma) psoriasis tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial malignant glioma bone giant cell tumor glioblastoma giant cell glioblastoma mixed glioma glioma lung adenocarcinoma medulloblastoma ovarian cancer astrocytoma (excluding glioblastoma) psoriasis tuberculosis chondroblastoma ependymoma Glioma of Brain, Familial intellectual disability lung cancer malignant mesothelioma pituitary cancer atopic eczema subependymal giant cell astrocytoma breast cancer cutaneous lupus erythematosus glioma susceptibility 1 invasive ductal breast carcinoma malignant colon neoplasm malignant pancreatic neoplasm non-small cell lung carcinoma plasma cell myeloma atypical teratoid rhabdoid tumor subependymoma breast carcinoma Down syndrome exocrine pancreatic carcinoma hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	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.