5Y1Z | pdb_00005y1z

Crystal structure of ZMYND8 PHD-BROMO-PWWP tandem in complex with Drebrin ADF-H domain

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PWWP	e5y1zD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
D	Bromodomain	e5y1zD1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
D	PHD_5	e5y1zD3	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
C	PWWP	e5y1zC3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PWWP	ECOD (1.6)
C	Bromodomain	e5y1zC1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
C	PHD_5	e5y1zC2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_5	ECOD (1.6)
B	Cofilin_ADF	e5y1zB1	A: a+b three layers	X: Gelsolin-like (From Topology)	H: Gelsolin-like (From Topology)	T: Gelsolin-like	F: Cofilin_ADF	ECOD (1.6)
A	Cofilin_ADF	e5y1zA1	A: a+b three layers	X: Gelsolin-like (From Topology)	H: Gelsolin-like (From Topology)	T: Gelsolin-like	F: Cofilin_ADF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.20.10	Alpha Beta	3-Layer(aba) Sandwich	Severin	Severin	CATH (4.3.0)
A	3.40.20.10	Alpha Beta	3-Layer(aba) Sandwich	Severin	Severin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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
C, D	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
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
A, B	PF00241	Cofilin/tropomyosin-type actin-binding protein (Cofilin_ADF)	Cofilin/tropomyosin-type actin-binding protein	Severs actin filaments and binds to actin monomers.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Protein kinase C-binding protein 1	protein binding binding protein domain specific binding histone H3K14ac reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity transcription corepressor activity transcription regulator activity transcription coregulator activity transcription factor binding DNA-binding transcription factor binding protein binding binding protein domain specific binding histone H3K14ac reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity transcription corepressor activity transcription regulator activity transcription coregulator activity transcription factor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K4me1 reader activity	cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process response to stimulus signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential cellular response to stimulus multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process response to stimulus signaling modulation of chemical synaptic transmission regulation of system process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential localization protein localization to chromatin protein localization to chromosome protein localization to organelle macromolecule localization intracellular protein localization regulation of cellular component organization dendritic spine maintenance positive regulation of cellular component organization cell projection organization cellular component maintenance positive regulation of biological process regulation of dendritic spine maintenance cellular component organization positive regulation of dendritic spine maintenance regulation of synapse structure or activity positive regulation of cell projection organization cellular component organization or biogenesis synapse organization positive regulation of cellular process plasma membrane bounded cell projection organization dendritic spine organization postsynapse organization regulation of cell projection organization regulation of postsynapse organization regulation of synapse organization cell junction organization neuron projection organization regulation of plasma membrane bounded cell projection organization regulation of developmental process cellular developmental process positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development positive regulation of developmental process neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development system development developmental process dendritic spine development nervous system development generation of neurons neuron development regulation of localization cellular localization regulation of protein localization postsynaptic density protein 95 clustering regulation of postsynaptic density protein 95 clustering postsynaptic density organization regulation of postsynaptic density organization regulation of protein localization to membrane postsynaptic membrane organization membrane organization localization within membrane protein localization to membrane regulation of organelle organization organelle organization regulation of cellular localization postsynaptic specialization organization double-strand break repair DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair negative regulation of locomotion regulation of cell motility negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion filopodium assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly positive regulation of filopodium assembly positive regulation of cellular component biogenesis regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cell projection assembly positive regulation of plasma membrane bounded cell projection assembly transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process positive regulation of metabolic process regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of DNA-templated transcription, elongation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression positive regulation of transcription by RNA polymerase II macromolecule biosynthetic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm nucleoplasm chromatin chromosome somatodendritic compartment cell projection dendrite dendritic tree neuron projection dendritic shaft plasma membrane bounded cell projection neuron spine synapse dendritic spine postsynapse cell junction site of DNA damage
A, B	Drebrin	molecular sequestering activity protein sequestering activity profilin binding protein binding binding cytoskeletal protein binding actin binding cell adhesion molecule binding cadherin binding	maintenance of protein location localization cellular localization maintenance of protein location in cell macromolecule localization cellular process intracellular protein localization maintenance of location maintenance of location in cell regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of developmental process maintenance of protein location localization cellular localization maintenance of protein location in cell macromolecule localization cellular process intracellular protein localization maintenance of location maintenance of location in cell regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation nervous system development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization regulation of synaptic plasticity trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission signaling cell-cell signaling chemical synaptic transmission cell communication positive regulation of synaptic plasticity synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication regulation of biological quality embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development cell communication by electrical coupling regulation of neuronal synaptic plasticity cell population proliferation neural precursor cell proliferation regulation of localization positive regulation of biological process receptor localization to synapse positive regulation of receptor localization to synapse regulation of receptor localization to synapse cell communication by chemical coupling organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization positive regulation of dendritic spine morphogenesis positive regulation of nervous system development positive regulation of dendritic spine development regulation of cell differentiation regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron projection morphogenesis regulation of dendrite morphogenesis regulation of synapse structure or activity positive regulation of cell projection organization synapse organization dendritic spine morphogenesis dendritic spine development postsynapse organization dendritic spine organization positive regulation of cell development regulation of postsynapse organization positive regulation of cell morphogenesis positive regulation of multicellular organismal process positive regulation of cellular component organization plasma membrane bounded cell projection morphogenesis regulation of dendritic spine development cell morphogenesis regulation of nervous system development positive regulation of neuron projection development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development dendrite morphogenesis positive regulation of dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis regulation of synapse organization cell junction organization regulation of dendritic spine morphogenesis neuron projection organization	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton actomyosin cell-cell junction anchoring junction gap junction somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cytoplasm growth cone axon distal axon site of polarized growth glutamatergic synapse postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse cell cortex cortical cytoskeleton cytosolic region postsynaptic cytosol cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR001965	Zinc finger, PHD-type	Domain
C, D	IPR057053	ZMYND11/ZMYD8, MYND zinc finger	Domain
C, D	IPR001487	Bromodomain	Domain
C, D	IPR000313	PWWP domain	Domain
C, D	IPR019787	Zinc finger, PHD-finger	Domain
C, D	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
C, D	IPR021931	MYND-type zinc finger-containing chromatin reader ZMYND8	Family
C, D	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
C, D	IPR002893	Zinc finger, MYND-type	Domain
C, D	IPR044075	PRKCBP1, PHD finger	Domain
C, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
C, D	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
C, D	IPR037967	ZMYND8, Bromo domain	Domain
C, D	IPR056987	ZMYND8, coiled-coil	Domain
A, B	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
A, B	IPR002108	Actin-depolymerising factor homology domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q9ULU4	astrocytic tumor invasive ductal breast carcinoma lung cancer osteosarcoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor bipolar disorder juvenile dermatomyositis lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis endogenous depression large cell medulloblastoma malignant mesothelioma astrocytic tumor invasive ductal breast carcinoma lung cancer osteosarcoma pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor bipolar disorder juvenile dermatomyositis lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis endogenous depression large cell medulloblastoma malignant mesothelioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
A, B	Pharos: Q16643	Alzheimer disease bipolar disorder inflammatory bowel disease Malignant neoplasm of breast neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia amyloidosis chronic kidney disease large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Alzheimer disease bipolar disorder inflammatory bowel disease Malignant neoplasm of breast neurodegenerative disease pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia amyloidosis chronic kidney disease large cell medulloblastoma medulloblastoma osteosarcoma primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Crohn disease lung cancer nephrolithiasis ovarian cancer psoriasis

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.