9ZQ9 | pdb_00009zq9

Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth P]	SCOP2B Superfamily	WGR domain-like	8074102	3000760	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Core histone-like	8034825	3001387	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Core histone-like	8034824	3001387	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Core histone-like	8066277	3001387	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Core histone-like	8067128	3001387	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Core histone-like	8067128	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)
H	RVP	e9zq9H1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
G	RVP	e9zq9G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
F	RVP	e9zq9F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
E	RVP	e9zq9E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
D	RVP	e9zq9D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
C	RVP	e9zq9C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
B	RVP	e9zq9B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)
A	RVP	e9zq9A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth P]	PF05406	WGR domain (WGR)	WGR domain	This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The ...	This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as Swiss:Q9JN21 and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain.	Domain
G, H	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
E, F	PF00125	Core histone H2A/H2B/H3/H4 domain (Histone)	Core histone H2A/H2B/H3/H4 domain		Domain
A, B	PF16211	C-terminus of histone H2A (Histone_H2A_C)	C-terminus of histone H2A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
M [auth J], N [auth I]	Ig-like domain-containing protein	-	-	-
L	DNA (128-MER)	-	-	-
K	DNA (69-MER)	-	-	-
J [auth M]	DNA (197-MER)	-	-	-
I [auth P]	Poly [ADP-ribose] polymerase 2	chromatin binding binding pentosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity transferase activity NAD+-protein mono-ADP-ribosyltransferase activity catalytic activity DNA binding damaged DNA binding nucleic acid binding NAD DNA ADP-ribosyltransferase activity ADP-D-ribose modification-dependent protein binding poly-ADP-D-ribose modification-dependent protein binding chromatin binding binding pentosyltransferase activity catalytic activity, acting on a protein glycosyltransferase activity transferase activity NAD+-protein mono-ADP-ribosyltransferase activity catalytic activity DNA binding damaged DNA binding nucleic acid binding NAD DNA ADP-ribosyltransferase activity ADP-D-ribose modification-dependent protein binding poly-ADP-D-ribose modification-dependent protein binding protein binding modification-dependent protein binding poly-ADP-D-ribose binding carbohydrate derivative binding NAD+-protein-aspartate ADP-ribosyltransferase activity NAD+ poly-ADP-ribosyltransferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups NAD+-protein-glutamate ADP-ribosyltransferase activity protein-containing complex binding nucleosome binding NAD+-protein-serine ADP-ribosyltransferase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA modification macromolecule modification metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA modification macromolecule modification metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA ADP-ribosylation neuron apoptotic process hippocampal neuron apoptotic process apoptotic process cell death programmed cell death DNA repair-dependent chromatin remodeling cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway signal transduction response to decreased oxygen levels response to nutrient levels response to oxygen levels response to abiotic stimulus response to oxygen-glucose deprivation DNA repair developmental process multi-multicellular organism process multicellular organismal process placenta development reproductive process maternal process involved in female pregnancy multicellular organismal reproductive process animal organ development developmental process involved in reproduction tissue development maternal placenta development anatomical structure development female pregnancy multi-organism reproductive process decidualization base-excision repair regulation of growth system process regulation of cardiac muscle tissue growth developmental growth regulation of system process regulation of cell differentiation muscle cell differentiation regulation of muscle hypertrophy muscle structure development positive regulation of developmental process multicellular organism development muscle adaptation cell differentiation regulation of organ growth regulation of heart growth cardiac muscle tissue growth muscle tissue development cardiac cell development positive regulation of developmental growth positive regulation of heart growth system development heart growth positive regulation of organ growth striated muscle hypertrophy positive regulation of muscle cell differentiation regulation of muscle cell differentiation regulation of response to stimulus positive regulation of muscle hypertrophy positive regulation of cardiac muscle tissue growth positive regulation of multicellular organismal process positive regulation of cell growth involved in cardiac muscle cell development striated muscle cell differentiation regulation of cellular component organization cellular developmental process regulation of developmental process positive regulation of cardiac muscle hypertrophy cardiac muscle cell development positive regulation of biological process cell development regulation of striated muscle cell differentiation organ growth cell growth striated muscle tissue development striated muscle cell development muscle cell development positive regulation of cell differentiation positive regulation of striated muscle cell differentiation cardiac muscle hypertrophy regulation of multicellular organismal process positive regulation of cellular process muscle hypertrophy regulation of muscle adaptation heart development regulation of multicellular organismal development regulation of developmental growth cardiac muscle tissue development developmental cell growth physiological muscle hypertrophy growth cardiac muscle cell differentiation regulation of cell growth involved in cardiac muscle cell development positive regulation of cell growth regulation of cell growth regulation of muscle system process muscle system process regulation of cardiac muscle hypertrophy cardiocyte differentiation circulatory system development cell growth involved in cardiac muscle cell development positive regulation of growth physiological cardiac muscle hypertrophy double-strand break repair protein poly-ADP-ribosylation protein metabolic process post-translational protein modification protein modification process protein auto-ADP-ribosylation	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 nucleoplasm site of DNA damage chromosome
G, H	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding 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	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex nuclear protein-containing complex RCAF complex protein-DNA complex nucleosome chromatin
E, F	Histone H3	DNA binding protein-containing complex binding binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding 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	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle RCAF complex protein-DNA complex nucleosome chromatin
C, D	Histone H2B	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity protein-containing complex binding structural molecule activity structural constituent of chromatin	cellular component organization chromatin organization cellular process cellular component organization or biogenesis	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, B	Histone H2A	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding 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 regulation of cellular 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 regulation of cellular process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule 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 developmental process muscle structure development multicellular organism development multicellular organismal process somatic muscle development larval somatic muscle development anatomical structure development larval development post-embryonic development	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region polytene chromosome band protein-containing complex protein-DNA complex nucleosome chromatin intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region polytene chromosome band protein-containing complex protein-DNA complex nucleosome chromatin membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth P]	IPR012317	Poly(ADP-ribose) polymerase, catalytic domain	Domain
I [auth P]	IPR050800	ADP-ribosyltransferase diphtheria toxin-like	Family
I [auth P]	IPR036616	Poly(ADP-ribose) polymerase, regulatory domain superfamily	Homologous Superfamily
I [auth P]	IPR036930	WGR domain superfamily	Homologous Superfamily
I [auth P]	IPR004102	Poly(ADP-ribose) polymerase, regulatory domain	Domain
I [auth P]	IPR008893	WGR domain	Domain
G, H	IPR009072	Histone-fold	Homologous Superfamily
G, H	IPR035425	CENP-T/Histone H4, histone fold	Domain
G, H	IPR001951	Histone H4	Family
G, H	IPR019809	Histone H4, conserved site	Conserved Site
G, H	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
E, F	IPR009072	Histone-fold	Homologous Superfamily
E, F	IPR000164	Histone H3/CENP-A	Family
E, F	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR055333	Histone H2B, conserved site	Conserved Site
C, D	IPR000558	Histone H2B	Family
C, D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B	IPR009072	Histone-fold	Homologous Superfamily
A, B	IPR002119	Histone H2A	Family
A, B	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B	IPR032454	Histone H2A, C-terminal domain	Domain
A, B	IPR032458	Histone H2A conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth P]	: Q9UGN5	lipodystrophy ovarian cancer atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma Malignant epithelial tumor of ovary peripheral neuropathy Takayasu arteritis malignant glioma ovarian epithelial tumor psoriasis lung cancer peripheral nervous system disease subependymal giant cell astrocytoma

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.