1XPX

Structural basis of prospero-DNA interaction; implications for transcription regulation in developing cells

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)
C [auth A]	d1xpxa_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Homeodomain	Homeo-prospero domain of Prospero protein	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	PROX1 domain C-terminal region-like	8056468	3002346	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Homeodomain-like	8002338	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)
C [auth A]	HPD	e1xpxA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: HPD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.10.10.500	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeo-prospero domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF05044	Homeo-prospero domain (HPD)	Homeo-prospero domain	Prospero is a large drosophila transcription factor protein that is expressed in all neural lineages of drosophila embryos. It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. Homolo ...	Prospero is a large drosophila transcription factor protein that is expressed in all neural lineages of drosophila embryos. It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. Homologues of prospero are found in a wide range of animals including humans with the highest level of similarity being found in the C-terminal 160 amino acids. This region was identified as containing an atypical homeobox domain followed by a prospero domain. However, the structure shows that these two regions form a single stable structural domain as defined here [1]. This homeo-prospero domain binds to DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	5'-D(APGPCPAPTPGPCPCPTPG)-3'	-	-	-
B [auth C]	5'-D(CPAPGPGPCPAPTPGPCPT)-3'	-	-	-
C [auth A]	Protein prospero	sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding sequence-specific DNA binding DNA binding binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding	developmental process neuroblast proliferation multicellular organismal process cell population proliferation cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development cell differentiation anatomical structure development cellular process neural precursor cell proliferation system development developmental process neuroblast proliferation multicellular organismal process cell population proliferation cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development cell differentiation anatomical structure development cellular process neural precursor cell proliferation system development head development central nervous system development animal organ development brain development protein localization localization cellular localization cellular macromolecule localization macromolecule localization regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation 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 cell cycle G1 to G0 transition cell cycle process negative regulation of neural precursor cell proliferation regulation of developmental process negative regulation of biological process regulation of neuroblast proliferation cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development negative regulation of neuroblast proliferation regulation of nervous system development negative regulation of neurogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation regulation of neural precursor cell proliferation negative regulation of cell population proliferation regulation of multicellular organismal development negative regulation of developmental process negative regulation of cell development regulation of cell population proliferation negative regulation of multicellular organismal process plasma membrane bounded cell projection organization cell projection organization neuron projection development axon development cellular component organization neuron differentiation neuron development cellular component organization or biogenesis regulation of localization regulation of protein localization regulation of protein localization to nucleus protein localization to nucleus regulation of cellular localization protein localization to organelle axonogenesis plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis cell fate commitment sensory organ development photoreceptor cell differentiation visual system development eye morphogenesis compound eye morphogenesis eye photoreceptor cell differentiation animal organ morphogenesis sensory system development eye development regulation of photoreceptor cell differentiation regulation of compound eye photoreceptor cell differentiation compound eye development sensory organ morphogenesis compound eye photoreceptor cell differentiation R7 cell differentiation regulation of R7 cell differentiation regulation of neuron differentiation negative regulation of cellular component organization regulation of cell projection organization negative regulation of axonogenesis regulation of neuron projection development regulation of cellular component organization regulation of axonogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis negative regulation of neuron projection development regulation of plasma membrane bounded cell projection organization 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 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 nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly positive regulation of DNA-templated transcription 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 RNA biosynthetic process gliogenesis glial cell differentiation dendrite guidance dendrite development dendrite morphogenesis neuron projection guidance neuroblast division asymmetric cell division asymmetric neuroblast division cell division regulation of molecular function regulation of DNA-binding transcription factor activity neuroblast fate commitment neuroblast differentiation asymmetric neuroblast division resulting in ganglion mother cell formation system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of taste cell fate determination ganglion mother cell fate determination compound eye photoreceptor fate commitment R7 cell fate commitment photoreceptor cell fate commitment eye photoreceptor cell fate commitment neuron fate commitment axon guidance peripheral nervous system development cell dedifferentiation dedifferentiation negative regulation of gene expression innervation nerve development axonogenesis involved in innervation behavior reproductive process male mating behavior multicellular organismal reproductive process male courtship behavior reproductive behavior courtship behavior mating behavior positive regulation of nervous system development positive regulation of cell population proliferation positive regulation of developmental process positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of cell development positive regulation of neural precursor cell proliferation positive regulation of multicellular organismal process positive regulation of neuroblast proliferation	cell periphery cellular anatomical structure cell cortex intracellular anatomical structure apical part of cell cell cortex region cytoplasm cytoplasmic region apical cortex basal part of cell basal cortex plasma membrane membrane membrane-bounded organelle cell periphery cellular anatomical structure cell cortex intracellular anatomical structure apical part of cell cell cortex region cytoplasm cytoplasmic region apical cortex basal part of cell basal cortex plasma membrane membrane membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR037131	Homeo-prospero domain superfamily	Homologous Superfamily
C [auth A]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C [auth A]	IPR023082	Homeo-prospero domain	Domain
C [auth A]	IPR039350	Prospero homeodomain family	Family

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.