8G87

Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)

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)
C [auth X]	SCOP2B Superfamily	lambda C1 repressor DNA-binding domain-like	8094725	3000119	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)
C [auth X]	PF00046	e8g87X1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
C [auth X]	PF00157	e8g87X2	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: PF00157	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth X]	PF00157	Pou domain - N-terminal to homeobox domain (Pou)	Pou domain - N-terminal to homeobox domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth I]	nMatn1 DNA (top strand)	-	-	-
B [auth J]	nMatn1 DNA (bottom strand)	-	-	-
C [auth X]	POU domain, class 5, transcription factor 1	DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA binding regulatory RNA binding miRNA binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular response to stimulus cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway response to stimulus signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP cellular process transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway endodermal-mesodermal cell signaling cell-cell signaling regulation of biosynthetic process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process developmental process anatomical structure morphogenesis anatomical structure development regulation of asymmetric cell division cell division asymmetric cell division regulation of cell division negative regulation of biological process negative regulation of miRNA transcription negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process regulation of miRNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process primary metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process miRNA transcription negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of miRNA metabolic process regulation of miRNA transcription multicellular organismal process formation of primary germ layer cellular developmental process embryonic morphogenesis embryo development gastrulation cell fate commitment involved in formation of primary germ layer multicellular organism development cell differentiation anatomical structure formation involved in morphogenesis cell fate commitment response to stress response to wounding heart development animal organ development cell fate determination cardiocyte differentiation circulatory system development cardiac cell fate determination cardiac cell fate commitment system development somatic stem cell population maintenance maintenance of cell number stem cell population maintenance endodermal cell fate specification cell fate specification tissue development endoderm development endoderm formation endodermal cell fate commitment endodermal cell differentiation regulation of cellular component organization protein-DNA complex organization cellular component organization chromatin organization DNA methylation-dependent heterochromatin formation chromatin remodeling cellular component organization or biogenesis regulation of heterochromatin formation regulation of chromatin organization heterochromatin formation protein-containing complex organization regulation of DNA methylation-dependent heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic facultative heterochromatin formation transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of cellular process positive regulation of canonical Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling negative regulation of transcription by RNA polymerase II embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development blastocyst development positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process heart induction regulation of developmental process heart morphogenesis specification of animal organ identity pattern specification process developmental induction positive regulation of developmental process animal organ morphogenesis animal organ formation regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of animal organ morphogenesis heart formation regionalization positive regulation of animal organ morphogenesis positive regulation of multicellular organismal process regulation of animal organ formation organ induction regulation of heart morphogenesis heart field specification	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol protein-containing complex transcription regulator complex nucleus membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cytosol protein-containing complex transcription regulator complex nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth X]	IPR001356	Homeobox domain	Domain
C [auth X]	IPR000327	POU-specific domain	Domain
C [auth X]	IPR013847	POU domain	Domain
C [auth X]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
C [auth X]	IPR017970	Homeobox, conserved site	Conserved Site
C [auth X]	IPR010982	Lambda repressor-like, DNA-binding domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth X]	Pharos: Q01860	gestational trophoblastic neoplasm amphetamine abuse embryonal neoplasm germ cell tumor Graves disease hepatitis B virus infection lung carcinoma myocardial infarction allergic rhinitis Neoplasms, Germ Cell and Embryonal prostate carcinoma breast disease skin basal cell carcinoma systemic sclerosis ulcerative colitis gestational trophoblastic neoplasm amphetamine abuse embryonal neoplasm germ cell tumor Graves disease hepatitis B virus infection lung carcinoma myocardial infarction allergic rhinitis Neoplasms, Germ Cell and Embryonal prostate carcinoma breast disease skin basal cell carcinoma systemic sclerosis ulcerative colitis congenital heart disease gestational trophoblastic disease head and neck squamous cell carcinoma HIV infectious disease maturity-onset diabetes of the young neoplasm of mature B-cells peripheral arterial disease autism spectrum disorder psoriasis squamous cell lung carcinoma cancer Takayasu arteritis chronic obstructive pulmonary disease cutaneous lupus erythematosus heart disease leprosy membranous glomerulonephritis plasma cell myeloma Behcet disease psoriatic arthritis Stevens-Johnson syndrome type 2 diabetes mellitus

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 R01GM133198.