5B3H | pdb_00005b3h

The crystal structure of the JACKDAW/IDD10 bound to the heterodimeric SHR-SCR complex

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)
F	ZF_C2H2	e5b3hF1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: ZF_C2H2	ECOD (1.6)
E [auth C]	ZF_C2H2	e5b3hC1	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: ZF_C2H2	ECOD (1.6)
B	GRAS	e5b3hB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: GRAS	ECOD (1.6)
D [auth E]	GRAS	e5b3hE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: GRAS	ECOD (1.6)
C [auth D]	GRAS	e5b3hD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: GRAS	ECOD (1.6)
A	GRAS	e5b3hA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: GRAS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth C]	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], F	PF22992	BIRD-IDD transcription factor, fourth C2HC zinc finger (C2CH-4th_BIRD-IDD)	BIRD-IDD transcription factor, fourth C2HC zinc finger	This C2HC zinc finger domain is found in the BIRD/INDETERMINATE DOMAIN (IDD) transcription factor family. Members of this BIRD/IDD family such as JACKDAW (JKD)/IDD10, BALDIBIS (BIB), MAGPIE (MGP)/IDD3 are required for asymmetric cell division of grou ...	This C2HC zinc finger domain is found in the BIRD/INDETERMINATE DOMAIN (IDD) transcription factor family. Members of this BIRD/IDD family such as JACKDAW (JKD)/IDD10, BALDIBIS (BIB), MAGPIE (MGP)/IDD3 are required for asymmetric cell division of ground tissue and QC specification by direct protein-protein interaction with SHR and/or SCR to control ground tissue patterning during root growth [1]. SHR-SCR functions as a transcription cofactor by binding to the zinc finger domains of these transcription factors. Members of the BIRD/IDD family contain 4 zinc finger domains, two classical C2H2 followed by two C2HC zinc finger domains. This entry represents the fourth C2HC zinc finger domain that is involved in interaction with SHR-SCR [1].	Domain
E [auth C], F	PF22995	BIRD-IDD transcription factor, third C2HC zinc finger (C2CH-3rd_BIRD-IDD)	BIRD-IDD transcription factor, third C2HC zinc finger	This C2HC zinc finger domain is found in the BIRD/INDETERMINATE DOMAIN (IDD) transcription factor family. Members of this BIRD/IDD family such as JACKDAW (JKD)/IDD10, BALDIBIS (BIB), MAGPIE (MGP)/IDD3 are required for asymmetric cell division of grou ...	This C2HC zinc finger domain is found in the BIRD/INDETERMINATE DOMAIN (IDD) transcription factor family. Members of this BIRD/IDD family such as JACKDAW (JKD)/IDD10, BALDIBIS (BIB), MAGPIE (MGP)/IDD3 are required for asymmetric cell division of ground tissue and QC specification by direct protein-protein interaction with SHR and/or SCR to control ground tissue patterning during root growth [1]. SHR-SCR functions as a transcription cofactor by binding to the zinc finger domains ot these transcription factors. Members of the BIRD/IDD family contain 4 zinc finger domains, two classical C2H2 followed by two C2HC zinc finger domains. This entry represents the third C2HC zinc finger domain that is involved in interaction with SHR-SCR and in DNA binding [1].	Domain
B, D [auth E]	PF03514	GRAS domain family (GRAS)	GRAS domain family	-	Family
A, C [auth D]	PF03514	GRAS domain family (GRAS)	GRAS domain family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C], F	Zinc finger protein JACKDAW	DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding DNA binding binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity transcription regulator activity DNA-binding transcription factor activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding sequence-specific DNA binding	developmental process multicellular organismal process epithelium development regulation of biological process regulation of multicellular organismal development regulation of cellular process cellular developmental process regulation of developmental process epidermal cell differentiation regulation of epidermal cell differentiation epidermis development biological regulation regulation of cell differentiation tissue development epithelial cell differentiation developmental process multicellular organismal process epithelium development regulation of biological process regulation of multicellular organismal development regulation of cellular process cellular developmental process regulation of developmental process epidermal cell differentiation regulation of epidermal cell differentiation epidermis development biological regulation regulation of cell differentiation tissue development epithelial cell differentiation regulation of epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development cellular process regulation of multicellular organismal process regulation of epidermis development 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process 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 regulation of growth regulation of developmental growth developmental growth growth regulation of meristem growth meristem development meristem maintenance meristem growth 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 RNA metabolic process positive regulation of RNA biosynthetic process cell division asymmetric cell division regulation of cell division localization protein localization to organelle macromolecule localization protein localization to nucleus intracellular protein localization plant organ development root development system development root system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B, D [auth E]	Protein SHORT-ROOT	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 regulator activity DNA-binding transcription factor activity	regulation of biological process regulation of cellular process regulation of hormone metabolic process regulation of hormone levels biological regulation cellular process metabolic process regulation of biological quality regulation of metabolic process hormone metabolic process developmental process multicellular organism development multicellular organismal process anatomical structure development regulation of biological process regulation of cellular process regulation of hormone metabolic process regulation of hormone levels biological regulation cellular process metabolic process regulation of biological quality regulation of metabolic process hormone metabolic process developmental process multicellular organism development multicellular organismal process anatomical structure development pattern specification process radial pattern formation regionalization plant organ development leaf development shoot system development phyllome development system development cell division asymmetric cell division negative regulation of biological process negative regulation of cell cycle negative regulation of mitotic cell cycle mitotic cell cycle regulation of mitotic cell cycle negative regulation of cellular process cell cycle regulation of cell cycle	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome late endosome nucleus
A, C [auth D]	Protein SCARECROW	transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding DNA binding binding nucleic acid binding	response to stimulus response to abiotic stimulus tropism response to external stimulus gravitropism response to gravity maintenance of protein location cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell response to stimulus response to abiotic stimulus tropism response to external stimulus gravitropism response to gravity maintenance of protein location cellular localization maintenance of protein location in nucleus protein localization to nucleus maintenance of location maintenance of location in cell localization maintenance of protein location in cell macromolecule localization protein localization to organelle cellular process maintenance of protein localization in organelle intracellular protein localization cell redox homeostasis cellular homeostasis homeostatic process developmental process cellular developmental process cell differentiation bundle sheath cell fate specification cell fate specification cell fate commitment multicellular organism development multicellular organismal process anatomical structure development pattern specification process radial pattern formation regionalization plant organ development leaf development shoot system development phyllome development system development cell division asymmetric cell division root development root system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C], F	IPR013087	Zinc finger C2H2-type	Domain
E [auth C], F	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
E [auth C], F	IPR055185	BIRD-IDD transcription factor, fourth C2HC zinc finger	Domain
E [auth C], F	IPR055187	BIRD-IDD transcription factor, third C2HC zinc finger	Domain
E [auth C], F	IPR055186	BIRD-IDD transcription factor, second C2H2 zinc finger	Domain
E [auth C], F	IPR031140	Protein indeterminate-domain 1-16	Family
B, D [auth E]	IPR005202	Transcription factor GRAS	Family
A, C [auth D]	IPR005202	Transcription factor GRAS	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.