7CWH | pdb_00007cwh

Structural basis of RACK7 PHD to read a pediatric glioblastoma-associated histone mutation H3.3G34R

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
B	PHD_5	e7cwhB1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	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	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001965	Zinc finger, PHD-type	Domain
B	IPR057053	ZMYND11/ZMYD8, MYND zinc finger	Domain
B	IPR001487	Bromodomain	Domain
B	IPR000313	PWWP domain	Domain
B	IPR019787	Zinc finger, PHD-finger	Domain
B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
B	IPR021931	MYND-type zinc finger-containing chromatin reader ZMYND8	Family
B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
B	IPR002893	Zinc finger, MYND-type	Domain
B	IPR044075	PRKCBP1, PHD finger	Domain
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
B	IPR037967	ZMYND8, Bromo domain	Domain
B	IPR056987	ZMYND8, coiled-coil	Domain
A	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A	IPR000164	Histone H3/CENP-A	Family
A	IPR009072	Histone-fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	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	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

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.