2DFY | pdb_00002dfy

Crystal structure of a cyclized protein fusion of LMO4 LIM domains 1 and 2 with the LIM interacting domain of LDB1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth C]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8032679	3000068	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8032684	3000068	SCOP2B (2022-06-29)
A [auth X]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8032679	3000068	SCOP2B (2022-06-29)
A [auth X]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8032684	3000068	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth C]	e2dfyC1	A: Tautomerase/MIF-like	X: Tautomerase/MIF	H: Tautomerase/MIF	T: Tautomerase_3	F:	ECOD (20:10:01)
B [auth C]	e2dfyC5	A: DP domain	X: DP domain	H: DP domain	T:	F:	ECOD (20:10:01)
A [auth X]	e2dfyX1	A: Tautomerase/MIF-like	X: Tautomerase/MIF	H: Tautomerase/MIF	T: Tautomerase_3	F:	ECOD (20:10:01)
A [auth X]	e2dfyX5	A: DP domain	X: DP domain	H: DP domain	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)
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], B [auth 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 [auth X], B [auth C]	fusion protein of LIM domain transcription factor LMO4 and LIM domain-binding protein 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding protein binding binding DNA-binding transcription factor binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process cellular developmental process cell differentiation in spinal cord nervous system development generation of neurons multicellular organism development central nervous system neuron differentiation neurogenesis spinal cord development central nervous system development neuron differentiation cell differentiation ventral spinal cord interneuron differentiation anatomical structure development developmental process multicellular organismal process cellular developmental process cell differentiation in spinal cord nervous system development generation of neurons multicellular organism development central nervous system neuron differentiation neurogenesis spinal cord development central nervous system development neuron differentiation cell differentiation ventral spinal cord interneuron differentiation anatomical structure development ventral spinal cord development cellular process system development embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure immune system development animal organ development gland development hematopoietic or lymphoid organ development thymus development immune system process heart development ventricular septum development circulatory system development cardiac septum development cardiac chamber development cardiac ventricle development spinal cord association neuron differentiation dorsal spinal cord development neuron fate specification neuron fate commitment cell fate specification spinal cord motor neuron cell fate specification spinal cord motor neuron differentiation cell fate commitment regulation of biological process regulation of cellular process regulation of developmental process regulation of cell fate commitment biological regulation regulation of cell fate specification cell activation regulation of cell activation regulation of multicellular organismal process 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 regulation of biosynthetic process 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 metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process 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 negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular 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 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 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 positive regulation of phosphorylation regulation of catalytic activity positive regulation of phosphate metabolic process regulation of transferase activity positive regulation of molecular function phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of phosphorus metabolic process phosphorylation positive regulation of catalytic activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of phosphorus metabolic process regulation of phosphorylation regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion	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 cell leading edge

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X], B [auth C]	IPR001781	Zinc finger, LIM-type	Domain
A [auth X], B [auth C]	IPR050945	LMO/RBTN Transcription Factors	Family

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.

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