6L6Y | pdb_00006l6y

Crystal Structure of Pluripotency Reprogramming Factor Sox17 mutant (Sox17EK) HMG Domain bound to DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2B Superfamily	HMG-box	8073218	3001368	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HMG-box	8073218	3001368	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 D]	ACS_CODH_B_C	e6l6yD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACS_CODH_B_C	ECOD (develop294)
F	ACS_CODH_B_C	e6l6yF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: ACS_CODH_B_C	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], F	PF00505	HMG (high mobility group) box (HMG_box)	HMG (high mobility group) box		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], F	Transcription factor SOX-17	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 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 transcription factor binding 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 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 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 beta-catenin binding	developmental process heart development multicellular organismal process animal organ development endocardium development circulatory system development anatomical structure morphogenesis multicellular organism development anatomical structure development anatomical structure formation involved in morphogenesis endocardium morphogenesis endocardium formation system development embryonic morphogenesis developmental process heart development multicellular organismal process animal organ development endocardium development circulatory system development anatomical structure morphogenesis multicellular organism development anatomical structure development anatomical structure formation involved in morphogenesis endocardium morphogenesis endocardium formation system development embryonic morphogenesis embryo development gastrulation ameboidal-type cell migration cell migration cellular process cell motility cell migration involved in gastrulation spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of protein stability biological regulation regulation of biological quality protein stabilization digestive system development foregut morphogenesis tube development digestive tract development tube morphogenesis embryonic foregut morphogenesis digestive tract morphogenesis protein destabilization regulation of biosynthetic process regulation of biological process regulation of cellular process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis common bile duct development hepaticobiliary system development regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation endodermal digestive tract morphogenesis embryonic organ development heart morphogenesis embryonic heart tube development embryonic heart tube morphogenesis animal organ morphogenesis epithelial tube morphogenesis embryonic organ morphogenesis epithelium development morphogenesis of an epithelium tissue development tissue morphogenesis RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription signal transduction involved in regulation of gene expression metanephros development kidney development renal system development cell fate determination cardiocyte differentiation cardiac cell fate determination cardiac cell fate commitment cell fate commitment endodermal cell fate determination formation of primary germ layer cell fate commitment involved in formation of primary germ layer endoderm development endoderm formation endodermal cell fate commitment endodermal cell differentiation positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process pattern specification process heart looping determination of bilateral symmetry determination of left/right symmetry specification of symmetry determination of heart left/right asymmetry regionalization left/right pattern formation gallbladder development blood vessel morphogenesis angiogenesis vasculature development blood vessel development chordate embryonic development cell morphogenesis inner cell mass cell differentiation in utero embryonic development blastocyst formation embryo development ending in birth or egg hatching inner cell mass cellular morphogenesis blastocyst development stem cell fate commitment stem cell differentiation stem cell fate specification cell fate specification catabolic process positive regulation of protein metabolic process macromolecule catabolic process protein metabolic process regulation of protein metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process cardiogenic plate morphogenesis ureter development regulation of stem cell proliferation stem cell proliferation cell population proliferation regulation of cell population proliferation vasculogenesis neural tube development anterior/posterior pattern specification nervous system development rostrocaudal neural tube patterning neural tube patterning stem cell division regulation of stem cell division cell division regulation of cell division endodermal cell fate specification response to chemical response to nitrogen compound response to alkaloid regulation of embryonic development regulation of multicellular organismal development regulation of multicellular organismal process endothelial cell differentiation endothelium development cardiac endothelial cell differentiation epithelial cell differentiation endocardial cell differentiation cardiac cell fate specification regulation of cell fate commitment regulation of cell fate specification regulation of cardiocyte differentiation regulation of cardiac cell fate specification response to peptide response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor outflow tract morphogenesis	protein-containing complex transcription regulator complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
B, E	DNA (5'-D(CPCPAPGPGPAPCPAPAPTPAPGPAPGPAPC)-3')	-	-	-
A, D [auth C]	DNA (5'-D(PGPGPTPCPTPCPTPAPTPTPGPTPCPCPTPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], F	IPR033392	Sox 7/17/18, central domain	Domain
C [auth D], F	IPR036910	High mobility group box domain superfamily	Homologous Superfamily
C [auth D], F	IPR021934	Sox, C-terminal	Domain
C [auth D], F	IPR050140	SRY-related HMG-box transcription factor-like	Family
C [auth D], F	IPR009071	High mobility group box domain	Domain

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.