2VI6 | pdb_00002vi6

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
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)
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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
C	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)
A	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)
F	Proteasome	e2vi6F1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
H	Proteasome	e2vi6H1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
G	Proteasome	e2vi6G1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
E	Proteasome	e2vi6E1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
D	Proteasome	e2vi6D1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
C	Proteasome	e2vi6C1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
B	Proteasome	e2vi6B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Proteasome	ECOD (v294.1)
A	V-set	e2vi6A1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

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	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity 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 chromatin binding	cellular response to stimulus cellular response to nitrogen compound response to ketone response to stimulus response to alcohol response to oxygen-containing compound response to nitrogen compound cellular response to ether cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to ether response to chemical response to rapamycin cellular response to stimulus cellular response to nitrogen compound response to ketone response to stimulus response to alcohol response to oxygen-containing compound response to nitrogen compound cellular response to ether cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to ether response to chemical response to rapamycin cellular process cellular response to rapamycin cellular response to ketone developmental process tissue regeneration developmental growth anatomical structure development growth regeneration response to peptide cellular response to erythropoietin response to cytokine cellular response to cytokine stimulus response to erythropoietin cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus signaling negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus negative regulation of cellular process signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of BMP signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to BMP regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cell growth multidimensional cell growth multicellular organismal process maintenance of cell number stem cell population maintenance stem cell division cell division regulation of developmental process cellular developmental process negative regulation of developmental process regulation of cell differentiation cell differentiation negative regulation of cell differentiation 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process response to bisphenol A 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 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 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 cell dedifferentiation dedifferentiation regulation of stem cell division regulation of cell division 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 stem cell differentiation	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001356	Homeodomain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017970	Homeobox, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050460	Distal-less homeobox transcription factors	Family

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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.