2VI6

Crystal Structure of the Nanog Homeodomain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2vi6a_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2vi6b_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d2vi6c_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d2vi6d_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d2vi6e_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d2vi6f_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d2vi6g_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H	d2vi6h_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	automated matches	automated matches	MOUSE (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
B	SCOP2 Family	Homeodomain	8071013	4000291	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Homeodomain-like	8071014	3000001	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	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)
A	Homeobox	e2vi6A1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
B	Homeobox	e2vi6B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
C	Homeobox	e2vi6C1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
D	Homeobox	e2vi6D1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
E	Homeobox	e2vi6E1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
F	Homeobox	e2vi6F1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
G	Homeobox	e2vi6G1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
H	Homeobox	e2vi6H1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
B	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
C	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
D	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
E	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
F	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
G	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
H	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00046	Homeodomain (Homeodomain)	Homeodomain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	HOMEOBOX PROTEIN NANOG	protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein 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 protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein 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 double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid 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 polymerase II sequence-specific DNA-binding transcription factor recruiting activity protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding chromatin binding transcription factor binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein 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 response to organic substance response to chemical negative regulation of stem cell differentiation developmental process cellular developmental process regulation of developmental process negative regulation of developmental process negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process negative regulation of cell differentiation multicellular organismal process negative regulation of cell fate specification endodermal cell fate specification embryo development negative regulation of cell fate commitment multicellular organism development regulation of endodermal cell differentiation anatomical structure development formation of primary germ layer regulation of endodermal cell fate specification regulation of cell fate commitment embryonic morphogenesis cell fate specification tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis negative regulation of endodermal cell differentiation negative regulation of endodermal cell fate specification endoderm development regulation of cell fate specification anatomical structure formation involved in morphogenesis endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation response to retinoic acid response to lipid response to oxygen-containing compound negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication regulation of signaling regulation of BMP signaling pathway negative regulation of response to stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction development of primary sexual characteristics reproductive structure development system development mesodermal cell differentiation mesoderm morphogenesis tissue morphogenesis mesodermal cell fate commitment mesoderm formation mesoderm development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process maintenance of cell number stem cell population maintenance cell dedifferentiation dedifferentiation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process stem cell division regulation of stem cell division cell division regulation of cell division somatic stem cell population maintenance transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process negative regulation of macromolecule metabolic process negative regulation of biosynthetic process positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle cell cycle regulation of cell cycle embryonic pattern specification pattern specification process positive regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nucleoplasm protein-containing complex protein-DNA complex chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001356	Homeobox domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017970	Homeobox, conserved site	Conserved Site

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.