4JCJ | pdb_00004jcj

Crystal structure of Isl1 LIM domains with Ldb1 LIM-interaction domain

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)
C	LIM_C	e4jcjC1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_C	ECOD (1.6)
C	LIM_N	e4jcjC3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_N	ECOD (1.6)
C	LIM_C_1	e4jcjC2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_C_1	ECOD (1.6)
C	KOG2181_1	e4jcjC4	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: KOG2181_1	ECOD (1.6)
B	LIM_C	e4jcjB1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_C	ECOD (1.6)
B	LIM_N	e4jcjB3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_N	ECOD (1.6)
B	LIM_C_1	e4jcjB2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_C_1	ECOD (1.6)
B	KOG2181_1	e4jcjB4	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: KOG2181_1	ECOD (1.6)
A	LIM_C	e4jcjA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_C	ECOD (1.6)
A	LIM_N	e4jcjA3	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_N	ECOD (1.6)
A	LIM_C_1	e4jcjA2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_C_1	ECOD (1.6)
A	KOG2181_1	e4jcjA4	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: KOG2181_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)
B	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)
A	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, C	PF17916	LIM interaction domain (LID) (LID)	LIM interaction domain (LID)	LIM-homeodomain (LIM-HD) proteins are transcription factors that are critical in the development of many cell types and tissues. The activity of LIM-HD proteins is dependent on the essential cofactor LIM domain-binding protein 1 (Ldb1). This entry re ...	LIM-homeodomain (LIM-HD) proteins are transcription factors that are critical in the development of many cell types and tissues. The activity of LIM-HD proteins is dependent on the essential cofactor LIM domain-binding protein 1 (Ldb1). This entry represents a 30-residue LIM interaction domain (LID) that binds to the LIM domains of all LIM-HD and closely related LIM-only (LMO) proteins. Isl1 (Insulin gene enhancer protein 1) and Isl2 each contain a LID-like sequence in their C-terminal regions, the Lhx3-binding domain (LBD), which binds the LIM domains Lhx3 and Lhx4 [1].	Domain
A, B, C	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, C	Insulin gene enhancer protein ISL-1,LIM domain-binding protein 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 core promoter sequence-specific DNA binding chromatin binding promoter-specific chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity 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 core promoter sequence-specific DNA binding chromatin binding promoter-specific chromatin 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 cation binding ion binding metal ion binding small molecule binding transcription factor binding protein binding bHLH transcription factor binding DNA-binding transcription factor binding LIM domain binding protein domain specific 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 RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding nuclear estrogen receptor binding transcription coactivator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein dimerization activity enzyme binding	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation heart development animal organ development circulatory system development interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 alpha production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of interleukin-1 production regulation of macromolecule metabolic process gene expression regulation of interleukin-1 alpha production macromolecule biosynthetic process regulation of gene expression interleukin-1 alpha production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway heart formation heart morphogenesis specification of animal organ identity pattern specification process regionalization anatomical structure morphogenesis 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 cell population proliferation negative regulation of signaling regulation of canonical Wnt signaling pathway regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway regulation of signaling 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 regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process epithelial cell apoptotic process positive regulation of type B pancreatic cell apoptotic process type B pancreatic cell apoptotic process apoptotic process programmed cell death 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 organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis cardioblast proliferation regulation of cardioblast proliferation regulation of secondary heart field cardioblast 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 head development forebrain development endocrine system development pituitary gland development gland development brain development diencephalon development central nervous system development 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 cell fate commitment 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 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 positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process 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 neuron fate commitment cell fate specification neuron fate specification 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 cell differentiation in spinal cord central nervous system neuron differentiation spinal cord development spinal cord motor neuron cell fate specification ventral spinal cord development spinal cord motor neuron differentiation 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 axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development 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 negative regulation of programmed cell death negative regulation of 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 tube development 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 amide transport 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 cell-substrate junction assembly cell adhesion cell junction assembly regulation of cell-substrate junction organization focal adhesion assembly regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization regulation of focal adhesion assembly regulation of cell-substrate junction assembly gastrulation with mouth forming second embryonic morphogenesis gastrulation homeostatic process primitive hemopoiesis myeloid cell homeostasis embryonic organ development erythrocyte homeostasis hemopoiesis erythrocyte differentiation embryonic hemopoiesis multicellular organismal-level homeostasis myeloid cell differentiation immune system process primitive erythrocyte differentiation homeostasis of number of cells organelle organization chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery regulation of cell development negative regulation of erythrocyte differentiation regulation of immune system process regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation regulation of erythrocyte differentiation regulation of hemopoiesis epithelium development epidermis development molting cycle process hair cycle skin development skin epidermis development hair follicle development molting cycle hair cycle process cerebellum development metencephalon development hindbrain development positive regulation of hemoglobin biosynthetic process hemoglobin metabolic process hemoglobin biosynthetic process regulation of hemoglobin biosynthetic process regulation of cell motility regulation of locomotion regulation of cell migration locomotion anterior/posterior axis specification anterior/posterior pattern specification axis specification positive regulation of cell adhesion somatic stem cell population maintenance maintenance of cell number stem cell population maintenance transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II DNA-templated transcription elongation epithelial structure maintenance anatomical structure homeostasis tissue homeostasis regulation of catalytic activity phosphorylation regulation of transferase activity regulation of molecular function regulation of kinase activity phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process phosphorus metabolic process cerebellar cortex morphogenesis hindbrain morphogenesis cerebellar Purkinje cell layer formation cerebellar Purkinje cell layer development cerebellar Purkinje cell differentiation cerebellar Purkinje cell layer morphogenesis cerebellar cortex formation cerebellum morphogenesis cerebellar cortex development cell differentiation in hindbrain	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen RNA polymerase II transcription regulator complex nuclear protein-containing complex beta-catenin-TCF complex cell leading edge

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001781	Zinc finger, LIM-type	Domain
A, B, C	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B, C	IPR047169	Insulin gene enhancer protein ISL-1/2-like	Family
A, B, C	IPR001356	Homeodomain	Domain
A, B, C	IPR017970	Homeobox, conserved site	Conserved Site
A, B, C	IPR047244	Insulin gene enhancer protein ISL-1/2-like, LIM domain1	Domain
A, B, C	IPR029005	LIM-domain binding protein/SEUSS	Family
A, B, C	IPR041363	LIM interaction 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.