5KDM | pdb_00005kdm

Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	BRNF1 DID-like	8047978	4005893	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PurM C-terminal domain-like	8106396	3000696	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8070527	3001387	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)
D	Tegument_dsDNA	e5kdmD1	A: a+b two layers	X: Alpha-beta plaits	H: PurM C-terminal domain-like (From Topology)	T: PurM C-terminal domain-like	F: Tegument_dsDNA	ECOD (1.6)
C	DAXX_histone_binding	e5kdmC1	A: alpha bundles	X: Death domain-associated protein 6 histone binding domain (From Topology)	H: Death domain-associated protein 6 histone binding domain (From Topology)	T: Death domain-associated protein 6 histone binding domain	F: DAXX_histone_binding	ECOD (1.6)
B	Histone_1	e5kdmB1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone_1	ECOD (1.6)
A	Histone	e5kdmA1	A: alpha arrays	X: Histone-like	H: Histone-related	T: Histone	F: Histone	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.20.58.2170	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
B	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)
A	1.10.20.10	Mainly Alpha	Orthogonal Bundle	Histone, subunit A	Histone, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF20920	Death domain-associated protein 6, histone binding domain (DAXX_hist_bd)	Death domain-associated protein 6, histone binding domain	This domain is found in the mammalian Death domain-associated protein 6 (DAXX) and in similar proteins from animals. DAXX is a transcription corepressor and a histone chaperone that shows specificity for the conserved histone H3.3. This entry represe ...	This domain is found in the mammalian Death domain-associated protein 6 (DAXX) and in similar proteins from animals. DAXX is a transcription corepressor and a histone chaperone that shows specificity for the conserved histone H3.3. This entry represents the histone binding domain, which adopts an all alpha-helical fold where the first two alpha-helices form a coiled coil [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Major tegument protein	carbon-nitrogen ligase activity, with glutamine as amido-N-donor phosphoribosylformylglycinamidine synthase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	nucleoside phosphate metabolic process nucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process nucleoside phosphate metabolic process nucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process purine nucleotide biosynthetic process biological process involved in interspecies interaction between organisms intracellular transport of virus viral process viral life cycle transport of virus biological process involved in symbiotic interaction	host cellular component cellular anatomical structure host cell other organism part host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle virion component viral tegument
C	Death domain-associated protein 6	p53 binding protein binding binding histone binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity enzyme regulator activity p53 binding protein binding binding histone binding molecular function inhibitor activity molecular function regulator activity transcription regulator inhibitor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity transcription coactivator activity transcription regulator activity transcription coregulator activity heat shock protein binding nuclear receptor binding nuclear androgen receptor binding transcription corepressor activity identical protein binding protein homodimerization activity protein dimerization activity kinase binding enzyme binding protein kinase binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding	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 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 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 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 negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus cellular response to arsenic-containing substance response to stimulus response to sodium arsenite response to arsenic-containing substance cellular response to chemical stimulus response to chemical cellular response to salt cellular response to sodium arsenite response to salt intracellular receptor signaling pathway response to lipid signaling hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to endogenous stimulus response to hormone response to steroid hormone androgen receptor signaling pathway signal transduction nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus cellular response to lipid nuclear receptor-mediated signaling pathway cellular response to heat cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death extrinsic apoptotic signaling pathway via death domain receptors cell surface receptor signaling pathway extrinsic apoptotic signaling pathway apoptotic signaling pathway response to copper ion cellular response to metal ion response to metal ion cellular response to copper ion 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 component organization or biogenesis nucleosome assembly nucleosome organization JNK cascade intracellular signaling cassette MAPK cascade regulation of protein modification process regulation of post-translational protein modification regulation of protein metabolic process regulation of protein ubiquitination protein ubiquitination macromolecule modification protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to topologically incorrect protein response to topologically incorrect protein cellular response to unfolded protein response to unfolded protein intrinsic apoptotic signaling pathway in response to oxidative stress neuron apoptotic process neuron intrinsic apoptotic signaling pathway in response to oxidative stress intrinsic apoptotic signaling pathway cellular response to nitrogen compound response to diamide cellular response to diamide response to nitrogen compound negative regulation of gene expression cellular response to cadmium ion response to cadmium ion	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 cytosol chromosome, centromeric region chromosome chromosomal region nucleoplasm nuclear body PML body
B	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding 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 organelle organization 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 organelle organization telomere organization chromosome organization localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane 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 CENP-A containing chromatin cellular anatomical structure membrane 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 CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A	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
D	IPR029062	Class I glutamine amidotransferase-like	Homologous Superfamily
D	IPR036676	PurM-like, C-terminal domain superfamily	Homologous Superfamily
D	IPR010918	PurM-like, C-terminal domain	Domain
D	IPR010077	Herpes virus tegument protein	Family
D	IPR036921	PurM-like, N-terminal domain superfamily	Homologous Superfamily
D	IPR024346	Tegument protein, herpes virus, N-terminal domain	Domain
C	IPR046378	Daxx, histone-binding domain	Domain
C	IPR031333	Daxx, N-terminal Rassf1C-interacting domain	Domain
C	IPR038298	Daxx, N-terminal domain superfamily	Homologous Superfamily
C	IPR046426	Daxx, histone-binding domain superfamily	Homologous Superfamily
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR035425	CENP-T/Histone H4, histone fold	Domain
B	IPR001951	Histone H4	Family
B	IPR019809	Histone H4, conserved site	Conserved Site
B	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	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
C	Pharos: Q9UER7	adrenal cortex carcinoma neuroendocrine neoplasm adrenal carcinoma cervical cancer lung cancer triple-negative breast carcinoma endogenous depression Malignant neoplasm of pancreas pancreatic endocrine carcinoma autism spectrum disorder glioblastoma malignant pancreatic neoplasm pancreatic neoplasm
B	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma ulcerative colitis allergic rhinitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma
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.