8Q36

Structure of Nucleosome Core with a Bound Metallopeptide Conjugate (Foamy Virus GAG Peptide-Au[I] Compound)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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)
B [auth AAA]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
F [auth EEE]	SCOP2B Superfamily	Core histone-like	8039340	3001387	SCOP2B (2022-06-29)
C [auth BBB]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
G [auth FFF]	SCOP2B Superfamily	Core histone-like	8070545	3001387	SCOP2B (2022-06-29)
D [auth CCC]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
H [auth GGG]	SCOP2B Superfamily	Core histone-like	8039342	3001387	SCOP2B (2022-06-29)
E [auth DDD]	SCOP2B Superfamily	Core histone-like	8039341	3001387	SCOP2B (2022-06-29)
I [auth HHH]	SCOP2B Superfamily	Core histone-like	8039341	3001387	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth AAA], F [auth EEE]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
C [auth BBB], G [auth FFF]	PF15511	Centromere kinetochore component CENP-T histone fold (CENP-T_C)	Centromere kinetochore component CENP-T histone fold	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...	CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].	Domain
D [auth CCC], H [auth GGG]	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family
D [auth CCC], H [auth GGG]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain
E [auth DDD], I [auth HHH]	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 [auth MMM]	GAG structural protein	DNA binding binding organic cyclic compound binding nucleic acid binding RNA binding	exit from host cell biological process involved in interspecies interaction between organisms viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus transport of virus transport of viral material towards nucleus exit from host cell biological process involved in interspecies interaction between organisms viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus transport of virus transport of viral material towards nucleus virion assembly viral budding viral budding via host ESCRT complex	host cellular component host intracellular part host cytoskeleton host cell part host intracellular region cellular anatomical entity host intracellular organelle host cell host intracellular membrane-bounded organelle host cell nucleus viral nucleocapsid viral capsid virion component host cell cytoplasm
B [auth AAA], F [auth EEE]	Histone H3.1	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 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 biosynthetic process 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 biosynthetic process cellular biosynthetic process cellular metabolic 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
C [auth BBB], G [auth FFF]	Histone H4	DNA binding binding organic cyclic compound 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 protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process regulation of megakaryocyte differentiation negative regulation of biological process megakaryocyte differentiation cell development regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation anatomical structure development negative regulation of cellular process 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 hemopoiesis negative regulation of developmental process regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	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 CENP-A containing chromatin 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 CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
D [auth CCC], H [auth GGG]	Histone H2A type 1-B/E	DNA binding binding organic cyclic compound binding nucleic acid binding protein-containing complex binding chromatin binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process cellular biosynthetic process negative regulation of cellular metabolic process cellular component organization chromatin organization chromatin remodeling negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process cellular process cellular biosynthetic process negative regulation of cellular metabolic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process heterochromatin formation epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression 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 protein localization protein localization to chromatin cellular localization protein localization to chromosome, centromeric region localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization protein localization to CENP-A containing chromatin	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome intracellular non-membrane-bounded organelle chromosome, centromeric region non-membrane-bounded organelle nucleus intracellular membrane-bounded organelle
E [auth DDD], I [auth HHH]	Histone H2B type 1-K	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus biological process involved in interspecies interaction between organisms innate immune response in mucosa response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus mucosal immune response organ or tissue specific immune response humoral immune response antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to Gram-negative bacterium defense response to bacterium response to bacterium antibacterial humoral response defense response to Gram-positive bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex protein-DNA complex nucleosome chromatin chromosome intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle extracellular region intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex protein-DNA complex nucleosome chromatin chromosome intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle extracellular region extracellular space membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
J [auth III]	DNA (145-MER)	-	-	-
K [auth JJJ]	DNA (145-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth MMM]	IPR004957	Gag polyprotein, N-terminal domain	Domain
A [auth MMM]	IPR049099	Gag polyprotein, C-terminal	Domain
A [auth MMM]	IPR049101	Gag polyprotein, conserved central domain	Domain
B [auth AAA], F [auth EEE]	IPR009072	Histone-fold	Homologous Superfamily
B [auth AAA], F [auth EEE]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth AAA], F [auth EEE]	IPR000164	Histone H3/CENP-A	Family
C [auth BBB], G [auth FFF]	IPR009072	Histone-fold	Homologous Superfamily
C [auth BBB], G [auth FFF]	IPR035425	CENP-T/Histone H4, histone fold	Domain
C [auth BBB], G [auth FFF]	IPR001951	Histone H4	Family
C [auth BBB], G [auth FFF]	IPR019809	Histone H4, conserved site	Conserved Site
C [auth BBB], G [auth FFF]	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
D [auth CCC], H [auth GGG]	IPR009072	Histone-fold	Homologous Superfamily
D [auth CCC], H [auth GGG]	IPR007125	Histone H2A/H2B/H3	Domain
D [auth CCC], H [auth GGG]	IPR002119	Histone H2A	Family
D [auth CCC], H [auth GGG]	IPR032454	Histone H2A, C-terminal domain	Domain
D [auth CCC], H [auth GGG]	IPR032458	Histone H2A conserved site	Conserved Site
E [auth DDD], I [auth HHH]	IPR009072	Histone-fold	Homologous Superfamily
E [auth DDD], I [auth HHH]	IPR007125	Histone H2A/H2B/H3	Domain
E [auth DDD], I [auth HHH]	IPR000558	Histone H2B	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth AAA], F [auth EEE]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer 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 allergic rhinitis ovarian cancer 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 astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma 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
C [auth BBB], G [auth FFF]	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease acute myeloid leukemia squamous cell lung carcinoma 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 acute myeloid leukemia squamous cell lung carcinoma 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 allergic rhinitis ulcerative colitis 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
D [auth CCC], H [auth GGG]	Pharos: P04908	juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma juvenile idiopathic arthritis pituitary cancer acute myeloid leukemia autism spectrum disorder hypertensive disorder lung adenocarcinoma medulloblastoma ovarian cancer psoriasis allergic rhinitis breast cancer invasive ductal breast carcinoma Juvenile psoriatic arthritis lung cancer non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma squamous cell lung carcinoma atypical teratoid rhabdoid tumor ductal breast carcinoma in situ lung carcinoma osteoarthritis
E [auth DDD], I [auth HHH]	Pharos: O60814	breast carcinoma autism spectrum disorder endogenous depression Mammary Neoplasms, Human breast cancer

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.