6YCQ | pdb_00006ycq

Crystal structure of the DNA binding domain of Arabidopsis thaliana Auxin Response Factor 1 (AtARF1) in complex with High Affinity DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
A	B3	e6ycqA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Type II restriction endonuclease effector domain	F: B3	ECOD (1.6)
A	Auxin_resp_C	e6ycqA3	A: beta barrels	X: SH3	H: Auxin response factor dimerization domain and ancillary domain (From Topology)	T: Auxin response factor dimerization domain and ancillary domain	F: Auxin_resp_C	ECOD (1.6)
A	Auxin_resp_N	e6ycqA1	A: beta barrels	X: SH3	H: Auxin response factor dimerization domain and ancillary domain (From Topology)	T: Auxin response factor dimerization domain and ancillary domain	F: Auxin_resp_N	ECOD (1.6)
B	B3	e6ycqB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Type II restriction endonuclease effector domain	F: B3	ECOD (1.6)
B	Auxin_resp_C	e6ycqB3	A: beta barrels	X: SH3	H: Auxin response factor dimerization domain and ancillary domain (From Topology)	T: Auxin response factor dimerization domain and ancillary domain	F: Auxin_resp_C	ECOD (1.6)
B	Auxin_resp_N	e6ycqB2	A: beta barrels	X: SH3	H: Auxin response factor dimerization domain and ancillary domain (From Topology)	T: Auxin response factor dimerization domain and ancillary domain	F: Auxin_resp_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF06507	Auxin response factor ancillary domain (ARF_AD)	Auxin response factor ancillary domain	This entry represents the C-terminal ancillary domain (AD) of Auxin Response Factor (ARF) transcription factors. ARFs are modular transcription factors consisting of three main regions: an N-terminal DNA-binding domain (DBD) which includes a B3 domai ...	This entry represents the C-terminal ancillary domain (AD) of Auxin Response Factor (ARF) transcription factors. ARFs are modular transcription factors consisting of three main regions: an N-terminal DNA-binding domain (DBD) which includes a B3 domain embedded within a dimerization domain (DD), followed by a middle region that determines transcriptional activity, and finally a C-terminal protein-protein interaction domain (PB1/III/IV). The ancillary domain represented by this entry forms a small five-stranded beta-barrel-like structure that tightly interacts with the dimerization domain.	Domain
A, B	PF02362	B3 DNA binding domain (B3)	B3 DNA binding domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	21-7B	-	-	-
C	21-7A	-	-	-
A, B	Auxin response factor 1	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sequence-specific DNA binding identical protein binding protein 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 cell death response to auxin response to stimulus response to hormone response to endogenous stimulus response to chemical auxin-activated signaling pathway cellular response to stimulus signaling hormone-mediated signaling pathway cellular response to auxin stimulus cell communication cellular response to endogenous stimulus cellular response to chemical stimulus signal transduction cellular response to hormone stimulus developmental process multicellular organismal process plant organ development plant organ senescence multicellular organism development anatomical structure development leaf development leaf senescence shoot system development phyllome development system development	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR033389	AUX/IAA domain	Domain
A, B	IPR015300	DNA-binding pseudobarrel domain superfamily	Homologous Superfamily
A, B	IPR003340	B3 DNA binding domain	Domain
A, B	IPR053793	PB1-like domain	Domain
A, B	IPR044835	Auxin response factor	Family
A, B	IPR010525	Auxin response factor 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.