4KOO | pdb_00004koo

Crystal Structure of WHY1 from Arabidopsis thaliana

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4kood1	Alpha and beta proteins (a+b)	ssDNA-binding transcriptional regulator domain	ssDNA-binding transcriptional regulator domain	Plant transcriptional regulator PBF-2	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
D	d4kood2	Artifacts	Tags	Tags	Tags	C-terminal Tags	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4kooc1	Alpha and beta proteins (a+b)	ssDNA-binding transcriptional regulator domain	ssDNA-binding transcriptional regulator domain	Plant transcriptional regulator PBF-2	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
C	d4kooc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
B	d4koob_	Alpha and beta proteins (a+b)	ssDNA-binding transcriptional regulator domain	ssDNA-binding transcriptional regulator domain	Plant transcriptional regulator PBF-2	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4kooa1	Alpha and beta proteins (a+b)	ssDNA-binding transcriptional regulator domain	ssDNA-binding transcriptional regulator domain	Plant transcriptional regulator PBF-2	automated matches	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d4kooa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	mouse-ear cress,thale-cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8088955	3000513	SCOP2B (2022-06-29)
C	SCOP2 Family	Plant transcriptional regulator PBF-2	8088954	4002553	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	ssDNA-binding transcriptional regulator domain	8088955	3000513	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8088955	3000513	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ssDNA-binding transcriptional regulator domain	8088955	3000513	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Sigma70_r2,Sigma70_ner	e4kooD1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
C	Sigma70_r2,Sigma70_ner	e4kooC1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
B	Sigma70_r2,Sigma70_ner	e4kooB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
A	Sigma70_r2,Sigma70_ner	e4kooA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (4.3.0)
C	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (4.3.0)
B	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (4.3.0)
A	2.30.31.10	Mainly Beta	Roll	Transcriptional Co-activator pc4	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08536	Whirly transcription factor (Whirly)	Whirly transcription factor	This family contains the plant whirly transcription factors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Single-stranded DNA-binding protein WHY1, chloroplastic	DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding mRNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding DNA binding binding nucleic acid binding transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA binding mRNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding telomeric DNA binding single-stranded DNA binding	cellular response to stimulus cellular response to salicylic acid stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation response to oxygen-containing compound cellular response to oxygen-containing compound response to salicylic acid cell communication cellular response to chemical stimulus response to chemical cellular process cellular response to stimulus cellular response to salicylic acid stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation response to oxygen-containing compound cellular response to oxygen-containing compound response to salicylic acid cell communication cellular response to chemical stimulus response to chemical cellular process signal transduction salicylic acid mediated signaling pathway primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair regulation of telomere maintenance regulation of cellular component organization telomere organization regulation of primary metabolic process cellular component organization cellular component organization or biogenesis regulation of nucleobase-containing compound metabolic process chromosome organization regulation of chromosome organization regulation of macromolecule metabolic process regulation of organelle organization telomere maintenance organelle organization regulation of metabolic process regulation of DNA metabolic process systemic acquired resistance biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to external biotic stimulus negative regulation of telomere maintenance negative regulation of biological process negative regulation of telomere maintenance via telomerase regulation of DNA biosynthetic process RNA-templated DNA biosynthetic process telomere maintenance via telomere lengthening negative regulation of chromosome organization negative regulation of nucleobase-containing compound metabolic process negative regulation of cellular component organization negative regulation of metabolic process regulation of telomere maintenance via telomere lengthening biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process DNA biosynthetic process negative regulation of DNA biosynthetic process negative regulation of telomere maintenance via telomere lengthening nucleic acid biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process telomere maintenance via telomerase nucleobase-containing compound biosynthetic process macromolecule biosynthetic process regulation of telomere maintenance via telomerase negative regulation of organelle organization negative regulation of biosynthetic process negative regulation of DNA metabolic process	membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid intracellular membraneless organelle nucleoid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure chloroplast nucleoid plastid stroma organelle membraneless organelle chloroplast stroma membrane-bounded organelle intracellular anatomical structure plastid plastid nucleoid intracellular membraneless organelle nucleoid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure chloroplast nucleoid plastid stroma organelle membraneless organelle chloroplast stroma cytoplasm chloroplast protein-containing complex catalytic complex DNA repair complex extracellular region chromosome chromosome, telomeric region chromosomal region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009044	ssDNA-binding transcriptional regulator	Homologous Superfamily
A, B, C, D	IPR013742	Whirly transcription factor	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.