1RUT | pdb_00001rut

Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A [auth X]	d1rutx1	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	LIM domain	LIM only 4 (Lmo4)	house mouse (Mus musculus ) [TaxId: 10090 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth X]	LIM	e1rutX1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM	ECOD (develop294)
A [auth X]	LAP1_C	e1rutX5	A: alpha bundles	X: DP domain	H: DP domain	T: DP domain	F: LAP1_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth X]	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 [auth X]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth X]	Fusion protein of Lmo4 protein and LIM domain-binding protein 1	protein binding binding LIM domain binding protein domain specific binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding transcription coactivator activity identical protein binding protein binding binding LIM domain binding protein domain specific binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromatin binding transcription coactivator activity identical protein binding protein homodimerization activity protein dimerization activity enzyme binding	regulation of cellular process negative regulation of biological process 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process 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 negative regulation of cellular process 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of cell-substrate adhesion regulation of cell adhesion cell-substrate adhesion regulation of cellular component biogenesis 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 developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis gastrulation with mouth forming second embryonic morphogenesis anatomical structure development embryo development gastrulation cellular developmental process homeostatic process primitive hemopoiesis cell development cell differentiation myeloid cell homeostasis embryonic organ development erythrocyte homeostasis hemopoiesis animal organ development 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 head development transcription by RNA polymerase II regulation of developmental process regulation of cell differentiation regulation of cell development negative regulation of erythrocyte differentiation negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development negative regulation of developmental 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 tissue development skin development skin epidermis development hair follicle development molting cycle hair cycle process nervous system development generation of neurons neurogenesis neuron differentiation system development brain development cerebellum development central nervous system development metencephalon development hindbrain development positive regulation of protein metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of hemoglobin biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process hemoglobin metabolic process hemoglobin biosynthetic process regulation of protein metabolic process regulation of hemoglobin biosynthetic process regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion anterior/posterior axis specification anterior/posterior pattern specification pattern specification process axis specification regionalization positive regulation of cell adhesion somatic stem cell population maintenance maintenance of cell number stem cell population maintenance cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction Wnt signaling pathway transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process DNA-templated transcription elongation positive regulation of RNA biosynthetic process negative regulation of transcription by RNA polymerase II 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 central nervous system neuron differentiation cerebellar Purkinje cell layer development cerebellar Purkinje cell differentiation cerebellar Purkinje cell layer morphogenesis cerebellar cortex formation cerebellum morphogenesis cerebellar cortex development anatomical structure formation involved in morphogenesis cell differentiation in hindbrain	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 intracellular organelle cellular anatomical structure organelle beta-catenin-TCF complex cell leading edge membrane-enclosed lumen 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 intracellular organelle cellular anatomical structure organelle beta-catenin-TCF complex cell leading edge membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X]	IPR029005	LIM-domain binding protein/SEUSS	Family
A [auth X]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.