2RGT | pdb_00002rgt

Crystal Structure of Lhx3 LIM domains 1 and 2 with the binding domain of Isl1

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	JmjC,JmjN	e2rgtA3	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: JmjC,JmjN	ECOD (v294.1)
A	PI3K_rbd,PIK3CG_ABD	e2rgtA1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (v294.1)
B	JmjC,JmjN	e2rgtB3	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: JmjC,JmjN	ECOD (v294.1)
B	PI3K_rbd,PIK3CG_ABD	e2rgtB1	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: PI3K_rbd,PIK3CG_ABD	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00412	LIM domain (LIM)	LIM domain	This family represents two copies of the LIM structural domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1	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 RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding transcription coregulator binding chromatin 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 transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding transcription coregulator binding chromatin binding promoter-specific chromatin binding RNA polymerase II transcription regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity transcription coactivator binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity core promoter sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding bHLH transcription factor binding LIM domain binding protein domain specific binding RNA polymerase II cis-regulatory region sequence-specific DNA binding nuclear receptor binding nuclear estrogen receptor binding	developmental process cellular developmental process cell differentiation cellular process multicellular organismal process cell differentiation in spinal cord neurogenesis multicellular organism development central nervous system neuron differentiation spinal cord development neuron differentiation anatomical structure development neuron fate specification system development developmental process cellular developmental process cell differentiation cellular process multicellular organismal process cell differentiation in spinal cord neurogenesis multicellular organism development central nervous system neuron differentiation spinal cord development neuron differentiation anatomical structure development neuron fate specification system development neuron fate commitment nervous system development cell fate specification spinal cord motor neuron cell fate specification generation of neurons central nervous system development ventral spinal cord development spinal cord motor neuron differentiation cell fate commitment placenta development animal organ development regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation 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 ear development sensory organ development inner ear development dorsal/ventral pattern formation pattern specification process regionalization somatic motor neuron differentiation medial motor column neuron differentiation tube development respiratory tube development lung development respiratory system development axonogenesis cell projection organization motor neuron axon guidance 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 anatomical structure morphogenesis neuron projection guidance neuron development head development forebrain development endocrine system development pituitary gland development gland development brain development diencephalon development cell fate commitment involved in pattern specification ventral spinal cord interneuron specification ventral spinal cord interneuron differentiation cell fate specification involved in pattern specification spinal cord dorsal/ventral patterning ventral spinal cord interneuron fate commitment spinal cord patterning biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process spinal cord association neuron differentiation dorsal spinal cord development positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II regulation of developmental process regulation of cell differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of neuron differentiation regulation of neuron differentiation heart development circulatory system development interleukin-1 production positive regulation of interleukin-1 alpha production regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production regulation of interleukin-1 production regulation of interleukin-1 alpha production interleukin-1 alpha production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production heart formation heart morphogenesis specification of animal organ identity anatomical structure formation involved in morphogenesis secondary heart field specification animal organ morphogenesis animal organ formation heart field specification regulation of macrophage colony-stimulating factor production positive regulation of granulocyte colony-stimulating factor production regulation of granulocyte colony-stimulating factor production positive regulation of macrophage colony-stimulating factor production granulocyte colony-stimulating factor production macrophage colony-stimulating factor production cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway 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 positive regulation of epithelial cell apoptotic process positive regulation of programmed cell death regulation of epithelial cell apoptotic process regulation of type B pancreatic cell apoptotic process positive regulation of apoptotic process epithelial cell apoptotic process positive regulation of type B pancreatic cell apoptotic process type B pancreatic cell apoptotic process regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cardioblast proliferation regulation of cardioblast proliferation regulation of secondary heart field cardioblast proliferation cell population proliferation cell proliferation involved in heart morphogenesis regulation of cell population proliferation regulation of cell proliferation involved in heart morphogenesis positive regulation of developmental process positive regulation of cell differentiation negative regulation of cell population proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation negative regulation of mesenchymal cell proliferation embryo development ending in birth or egg hatching pharyngeal system development chordate embryonic development embryo development regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production cardiac chamber morphogenesis cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis mesenchyme development mesenchymal cell differentiation tissue development regulation of calcium ion import regulation of calcium ion transport regulation of localization positive regulation of calcium ion transport positive regulation of calcium ion import transport regulation of transport regulation of monoatomic ion transport establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport intracellular receptor signaling pathway response to lipid negative regulation of intracellular signal transduction hormone-mediated signaling pathway intracellular signal transduction negative regulation of intracellular steroid hormone receptor signaling pathway cellular response to endogenous stimulus response to hormone regulation of intracellular signal transduction response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway regulation of intracellular estrogen receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus negative regulation of intracellular estrogen receptor signaling pathway steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus estrogen receptor signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid nuclear receptor-mediated signaling pathway sensory system development cell fate determination cardiocyte differentiation cardiac cell fate determination cardiac cell fate commitment negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation ventricular cardiac muscle tissue morphogenesis striated muscle tissue development muscle structure development ventricular cardiac muscle tissue development muscle tissue development muscle organ development cardiac muscle tissue development muscle tissue morphogenesis tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis cardiac ventricle development muscle organ morphogenesis cardiac right ventricle morphogenesis heart process system process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation cardiac conduction regulation of biological quality regulation of heart rate by cardiac conduction heart contraction blood circulation regulation of heart rate cardiac atrium morphogenesis cardiac atrium development atrial septum morphogenesis atrial septum development regulation of vascular endothelial growth factor production vascular endothelial growth factor production positive regulation of vascular endothelial growth factor production cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to growth factor regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition epithelial to mesenchymal transition interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production retinal ganglion cell axon guidance regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of smoothened signaling pathway regulation of smoothened signaling pathway smoothened signaling pathway positive regulation of signaling regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production stem cell development neural crest cell differentiation neural crest cell development mesenchymal cell migration stem cell differentiation ameboidal-type cell migration cell migration cell motility neural crest cell migration neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process positive regulation of cell population proliferation pancreas development trigeminal nerve development nerve development cranial nerve development peripheral nervous system neuron development peripheral nervous system development peripheral nervous system neuron differentiation peripheral nervous system neuron axonogenesis mesenchyme morphogenesis endocardial cushion morphogenesis endocardial cushion development angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis positive regulation of angiogenesis vasculature development positive regulation of vasculature development regulation of angiogenesis cardiac muscle cell development muscle cell differentiation cardiac pacemaker cell development striated muscle cell development muscle cell development sinoatrial node cell differentiation sinoatrial node development cardiac cell development cardiac conduction system development cardiac muscle cell differentiation atrial cardiac muscle tissue development sinoatrial node cell development striated muscle cell differentiation cardiac pacemaker cell differentiation granulocyte macrophage colony-stimulating factor production positive regulation of protein metabolic process positive regulation of granulocyte macrophage colony-stimulating factor production protein metabolic process regulation of granulocyte macrophage colony-stimulating factor production regulation of protein metabolic process regeneration response to axon injury neuron projection regeneration axon regeneration cellular response to stress response to wounding cardiac muscle cell myoblast differentiation cardioblast differentiation myoblast differentiation regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization positive regulation of insulin secretion intracellular protein localization regulation of peptide hormone secretion regulation of hormone levels positive regulation of peptide hormone secretion establishment of protein localization to extracellular region protein secretion regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion positive regulation of secretion by cell hormone secretion protein localization to extracellular region positive regulation of protein transport peptide secretion regulation of secretion by cell secretion by cell positive regulation of hormone secretion positive regulation of secretion signal release positive regulation of peptide secretion secretion regulation of peptide transport regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion peptide transport protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport insulin secretion innervation visceral motor neuron differentiation response to glucocorticoid cellular response to glucocorticoid stimulus cellular response to corticosteroid stimulus response to corticosteroid regulation of type II interferon production type II interferon production positive regulation of type II interferon production	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 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 membraneless organelle intracellular membraneless organelle chromatin chromosome cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017970	Homeobox, conserved site	Conserved Site
A, B	IPR049594	LIM/homeobox protein Lhx3/4-like, LIM domain 2	Domain
A, B	IPR001781	Zinc finger, LIM-type	Domain
A, B	IPR050453	LIM/homeobox transcription factors	Family
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR049593	LIM/homeobox protein Lhx3, LIM domain 1	Domain
A, B	IPR001356	Homeodomain	Domain
A, B	IPR001781	Zinc finger, LIM-type	Domain
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR047169	Insulin gene enhancer protein ISL-1/2-like	Family
A, B	IPR001356	Homeodomain	Domain
A, B	IPR017970	Homeobox, conserved site	Conserved Site
A, B	IPR047244	Insulin gene enhancer protein ISL-1/2-like, LIM domain1	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.