4UUS

CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE UBDA MOTIF

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Homeodomain-like	8057619	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homeodomain-like	8057619	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8057620	3000001	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Homeodomain-like	8057620	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	PF00046	e4uusA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
E	PF00046	e4uusE1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
B	PF05920	e4uusB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF05920	ECOD (1.6)
F	PF05920	e4uusF1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF05920	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)
E	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)
F	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, E	PF00046	Homeodomain (Homeodomain)	Homeodomain	-	Domain
B, F	PF05920	Homeobox KN domain (Homeobox_KN)	Homeobox KN domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	HOMEOTIC PROTEIN ULTRABITHORAX	protein binding binding protein domain specific binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein binding binding protein domain specific binding DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription factor binding transcription coregulator binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process 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 organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process 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 organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound 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 cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process developmental process multicellular organismal process regulation of developmental process animal organ development positive regulation of biological process muscle structure development positive regulation of developmental process positive regulation of muscle organ development regulation of muscle organ development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal process muscle organ development heart development multicellular organism development circulatory system development system development digestive system development tube development midgut development digestive tract development blastoderm segmentation embryonic pattern specification specification of segmental identity, thorax segmentation pattern specification process embryo development regionalization specification of segmental identity, trunk trunk segmentation segment specification somatic muscle development respiratory system development open tracheal system development cellular developmental process regulation of cell fate commitment cell fate specification regulation of cell fate specification cell differentiation cell fate commitment Malpighian tubule development epithelium development tissue development renal system development anterior Malpighian tubule development renal tubule development regulation of growth regulation of developmental growth regulation of imaginal disc growth developmental growth growth imaginal disc growth imaginal disc development imaginal disc morphogenesis appendage development post-embryonic appendage morphogenesis leg disc development instar larval or pupal development metamorphosis leg disc morphogenesis imaginal disc-derived appendage morphogenesis anatomical structure morphogenesis appendage morphogenesis imaginal disc-derived appendage development instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development animal organ morphogenesis imaginal disc-derived leg morphogenesis haltere disc development haltere development cell fate determination cell fate commitment involved in pattern specification anterior/posterior pattern specification dorsal vessel aortic cell fate commitment cardiocyte differentiation embryonic heart tube anterior/posterior pattern specification cardiac cell fate commitment muscle cell fate specification muscle cell fate commitment muscle cell differentiation 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 RNA metabolic process positive regulation of DNA-templated transcription positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process formation of primary germ layer embryonic morphogenesis gastrulation endoderm development anatomical structure formation involved in morphogenesis endoderm formation transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II specification of animal organ identity animal organ formation mesodermal cell differentiation mesoderm morphogenesis mesodermal cell fate commitment mesoderm formation mesodermal cell fate specification mesoderm development cell fate commitment involved in formation of primary germ layer tissue morphogenesis	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity chromosomal region polytene chromosome band non-membrane-bounded organelle protein-containing complex transcription regulator complex transcription repressor complex protein-DNA complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle polytene chromosome chromosome cellular anatomical entity chromosomal region polytene chromosome band non-membrane-bounded organelle protein-containing complex transcription regulator complex transcription repressor complex protein-DNA complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B, F	HOMEOTIC PROTEIN EXTRADENTICLE	transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid 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 organic cyclic compound binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein binding protein dimerization activity transcription coactivator activity DNA-binding transcription factor activity transcription factor binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription factor binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development anatomical structure morphogenesis animal organ morphogenesis gland development pattern specification process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development anatomical structure morphogenesis animal organ morphogenesis gland development pattern specification process salivary gland development formation of anatomical boundary salivary gland boundary specification regionalization anatomical structure formation involved in morphogenesis formation of animal organ boundary animal organ formation exocrine system development muscle structure development somatic muscle development regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process regulation of cell fate commitment biological regulation cell fate specification regulation of cell fate specification cell differentiation cellular process cell fate commitment embryonic organ development embryo development peripheral nervous system development 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 organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular 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 biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process oenocyte development oenocyte differentiation cell development sensory organ development eye development visual system development sensory system development transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II generation of neurons neurogenesis neuron differentiation neuron development	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm protein-DNA complex
C, G	5'-D(GPTPCPGPCPCPAPTPAPAPAPTPCPAP*C)-3'	-	-	-
D, H	5'-D(APCPGPTPGPAPTPTPTPAPTPGPGPCP*G)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR001356	Homeobox domain	Domain
A, E	IPR001827	Homeobox protein, antennapedia type, conserved site	Conserved Site
A, E	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
A, E	IPR017970	Homeobox, conserved site	Conserved Site
A, E	IPR020479	Homeobox domain, metazoa	Domain
B, F	IPR001356	Homeobox domain	Domain
B, F	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
B, F	IPR017970	Homeobox, conserved site	Conserved Site
B, F	IPR005542	PBX, PBC domain	Domain
B, F	IPR008422	Homeobox KN domain	Domain

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.