3MMK | pdb_00003mmk

The structural basis for partial redundancy in a class of transcription factors, the lim-homeodomain proteins, in neural cell type specification

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)
B	LIM_C	e3mmkB3	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_1	e3mmkB4	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_N_1	ECOD (1.6)
B	LIM_N	e3mmkB1	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	e3mmkA3	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_1	e3mmkA5	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_N_1	ECOD (1.6)
A	LIM_N	e3mmkA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: LIM_N	ECOD (1.6)

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)
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	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 Lhx4, linker, Insulin gene enhancer protein ISL-2	sequence-specific DNA binding DNA binding binding nucleoside phosphate binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding sequence-specific DNA binding DNA binding binding nucleoside phosphate binding nucleotide binding nucleic acid binding heterocyclic compound binding methyl-CpG binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding sequence-specific double-stranded DNA binding double-stranded DNA 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	developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis placenta 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 developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis placenta 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 cellular process apoptotic process programmed cell death multicellular organismal process cellular developmental process cell differentiation in spinal cord nervous system development generation of neurons multicellular organism development neurogenesis central nervous system neuron differentiation spinal cord development central nervous system development neuron differentiation cell differentiation somatic motor neuron differentiation medial motor column neuron differentiation ventral spinal cord development spinal cord motor neuron differentiation 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 neuron projection guidance neuron development 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 neuron fate specification neuron fate commitment cell fate specification spinal cord motor neuron cell fate specification cell fate commitment retinal ganglion cell axon guidance visceral motor neuron differentiation 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR047956	LIM/homeobox protein Lhx4, LIM domain 1	Domain
A, B	IPR017970	Homeobox, conserved site	Conserved Site
A, B	IPR049594	LIM/homeobox protein Lhx3/4-like, LIM domain 2	Domain
A, B	IPR001356	Homeodomain	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	IPR047169	Insulin gene enhancer protein ISL-1/2-like	Family
A, B	IPR017970	Homeobox, conserved site	Conserved Site
A, B	IPR047244	Insulin gene enhancer protein ISL-1/2-like, LIM domain1	Domain
A, B	IPR001356	Homeodomain	Domain
A, B	IPR001781	Zinc finger, LIM-type	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.