9YZQ | pdb_00009yzq

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TGATGAGCAG and loaded with Engrailed homeodomain enhanced Green fluorescent protein fusion

External Resource: Annotation

Domain Annotation: SCOP2 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)
D	SCOP2B Superfamily	Homeodomain-like	8054195	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002855	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002854	3000034	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D	PF10525	Engrailed homeobox C-terminal signature domain (Engrail_1_C_sig)	Engrailed homeobox C-terminal signature domain	Engrailed homeobox proteins are characterised by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for th ...	Engrailed homeobox proteins are characterised by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	Segmentation polarity homeobox protein engrailed,Green fluorescent protein	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 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 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 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 transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding	developmental process multicellular organismal process blastoderm segmentation embryonic pattern specification segmentation pattern specification process embryo development regionalization multicellular organism development anatomical structure development segment polarity determination periodic partitioning imaginal disc morphogenesis animal organ development developmental process multicellular organismal process blastoderm segmentation embryonic pattern specification segmentation pattern specification process embryo development regionalization multicellular organism development anatomical structure development segment polarity determination periodic partitioning imaginal disc morphogenesis animal organ development wing disc development instar larval or pupal development metamorphosis anatomical structure morphogenesis wing disc morphogenesis imaginal disc development instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development animal organ morphogenesis regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process trunk segmentation head development head segmentation anterior head development anterior head segmentation cellular developmental process nervous system development generation of neurons neurogenesis neuron differentiation cell differentiation system development genital disc development gonad development reproductive system development reproductive process sex differentiation developmental process involved in reproduction development of primary sexual characteristics reproductive structure development analia development neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of neuron apoptotic process compartment pattern specification anterior/posterior pattern specification posterior compartment specification central nervous system development ventral midline development anterior/posterior pattern specification, imaginal disc genital disc pattern formation imaginal disc pattern formation genital disc anterior/posterior pattern formation imaginal disc-derived wing morphogenesis imaginal disc-derived wing vein specification appendage development post-embryonic appendage morphogenesis imaginal disc-derived appendage morphogenesis appendage morphogenesis imaginal disc-derived appendage development spiracle morphogenesis, open tracheal system respiratory system development open tracheal system development axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development anterior/posterior lineage restriction, imaginal disc imaginal disc lineage restriction neuroblast fate commitment neuroblast differentiation cell fate determination neuroblast fate determination cell fate commitment wing disc anterior/posterior pattern formation wing disc pattern formation 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 transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule 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 RNA metabolic process posterior head segmentation 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	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
C	Replication initiation protein	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding	cellular process plasmid maintenance nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
B	DNA (31-MER)	-	-	-
A	DNA (31-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR017970	Homeobox, conserved site	Conserved Site
D	IPR050720	Engrailed Homeobox Transcription Factors	Family
D	IPR019737	Homeobox engrailed-type, conserved site	Conserved Site
D	IPR000747	Homeodomain engrailed	Domain
D	IPR009057	Homedomain-like superfamily	Homologous Superfamily
D	IPR019549	Homeobox engrailed, C-terminal	Domain
D	IPR000047	Helix-turn-helix motif	Conserved Site
D	IPR020479	Homeodomain, metazoa	Domain
D	IPR001356	Homeodomain	Domain
C	IPR000525	Initiator Rep protein, WH1 domain	Domain
C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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.