6IIS

Complex structure of the HRP3 PWWP domain with both a 16-bp TA-rich DNA and an H3K36me3-containing histone peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8100746	3000404	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tudor/PWWP/MBT domain-like	8100746	3000404	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PWWP	e6iisA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
B	PWWP	e6iisB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
E, F	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, B	Hepatoma-derived growth factor-related protein 3	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity	protein polymerization protein-containing complex organization microtubule cytoskeleton organization microtubule polymerization cellular component organization cellular component biogenesis organelle organization microtubule polymerization or depolymerization cellular component assembly protein-containing complex assembly cellular process microtubule-based process cellular component organization or biogenesis supramolecular fiber organization protein polymerization protein-containing complex organization microtubule cytoskeleton organization microtubule polymerization cellular component organization cellular component biogenesis organelle organization microtubule polymerization or depolymerization cellular component assembly protein-containing complex assembly cellular process microtubule-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization regulation of cytoskeleton organization regulation of microtubule polymerization or depolymerization regulation of cellular component organization regulation of cellular process negative regulation of microtubule depolymerization negative regulation of biological process protein-containing complex disassembly regulation of protein-containing complex disassembly regulation of microtubule depolymerization negative regulation of protein-containing complex disassembly negative regulation of cellular process negative regulation of supramolecular fiber organization cellular component disassembly regulation of biological process negative regulation of cellular component organization negative regulation of microtubule polymerization or depolymerization regulation of protein depolymerization negative regulation of cytoskeleton organization biological regulation regulation of microtubule-based process regulation of organelle organization negative regulation of protein depolymerization negative regulation of organelle organization microtubule depolymerization regulation of supramolecular fiber organization protein depolymerization regulation of microtubule cytoskeleton organization developmental process multicellular organismal process plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development protein-DNA complex organization chromatin organization chromatin remodeling	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol extracellular region membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol extracellular region membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C, D	16-bp TA-rich DNA	-	-	-
E, F	H3K36me3 peptide	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity 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 organic substance metabolic process 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression 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 metabolic process	membrane cellular anatomical entity 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 membrane cellular anatomical entity 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 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, B	IPR000313	PWWP domain	Domain
E, F	IPR009072	Histone-fold	Homologous Superfamily
E, F	IPR007125	Histone H2A/H2B/H3	Domain
E, F	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y3E1	ovarian cancer pilocytic astrocytoma astrocytic tumor breast cancer gastric cancer juvenile dermatomyositis lung cancer malignant ependymoma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma psoriasis attention deficit hyperactivity disorder, inattentive type chronic obstructive pulmonary disease gastric carcinoma large cell medulloblastoma ovarian cancer pilocytic astrocytoma astrocytic tumor breast cancer gastric cancer juvenile dermatomyositis lung cancer malignant ependymoma nasopharyngeal carcinoma pancreatic intraductal papillary-mucinous carcinoma psoriasis attention deficit hyperactivity disorder, inattentive type chronic obstructive pulmonary disease gastric carcinoma large cell medulloblastoma lung carcinoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis atypical teratoid rhabdoid tumor Duchenne muscular dystrophy glioblastoma lung adenocarcinoma malignant colon neoplasm malignant mesothelioma
E, F	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F	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.