1U3C

Crystal Structure of the PHR domain of Cryptochrome 1 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)
A	d1u3ca1	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome C-terminal domain	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)
A	d1u3ca2	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	Cryptochrome	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)
A	SCOP2B Superfamily	Cryptochrome/photolyase FAD-binding domain	8040698	3000930	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cryptochrome/photolyase, N-terminal domain	8040699	3001644	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)
A	FAD_binding_7	e1u3cA1	A: alpha complex topology	X: Cryptochrome/photolyase FAD-binding domain-related (From Homology)	H: Cryptochrome/photolyase FAD-binding domain-related	T: Cryptochrome/photolyase FAD-binding domain	F: FAD_binding_7	ECOD (1.6)
A	DNA_photolyase	e1u3cA2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.10.579.10	Mainly Alpha	Orthogonal Bundle	DNA Cyclobutane Dipyrimidine Photolyase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
A	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cryptochrome 1 apoprotein	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding adenyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding purine nucleotide binding adenyl nucleotide binding ATP binding carbohydrate derivative binding ribonucleotide binding catalytic activity, acting on a protein protein kinase activity phosphotransferase activity, alcohol group as acceptor blue light photoreceptor activity molecular transducer activity photoreceptor activity signaling receptor activity cation binding metal ion binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	response to acid chemical response to stimulus response to stress response to chemical response to oxygen-containing compound response to abiotic stimulus response to water response to water deprivation response to light stimulus response to radiation response to blue light cellular response to stimulus regulation of biological process regulation of cellular process response to acid chemical response to stimulus response to stress response to chemical response to oxygen-containing compound response to abiotic stimulus response to water response to water deprivation response to light stimulus response to radiation response to blue light cellular response to stimulus regulation of biological process regulation of cellular process intracellular receptor signaling pathway signaling biological regulation cellular response to radiation intracellular signal transduction cellular response to environmental stimulus cell communication cellular response to light stimulus cellular process cellular response to abiotic stimulus signal transduction blue light signaling pathway cellular response to blue light multicellular organismal process regulation of developmental process negative regulation of biological process negative regulation of post-embryonic development post-embryonic root development multicellular organism development regulation of lateral root development regulation of post-embryonic root development anatomical structure development lateral root development regulation of multicellular organismal process post-embryonic development negative regulation of lateral root development regulation of root development root development system development developmental process regulation of multicellular organismal development plant organ development negative regulation of developmental process regulation of post-embryonic development post-embryonic plant organ development negative regulation of multicellular organismal process root system development positive regulation of shade avoidance positive regulation of biological process regulation of response to red or far red light response to red or far red light positive regulation of response to stimulus regulation of shade avoidance regulation of response to stimulus shade avoidance photomorphogenesis regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of growth regulation of cellular component organization developmental growth unidimensional cell growth cell morphogenesis cell growth regulation of cell morphogenesis cellular component organization cellular component organization or biogenesis regulation of anatomical structure morphogenesis regulation of developmental growth growth regulation of cell growth developmental growth involved in morphogenesis regulation of unidimensional cell growth anatomical structure morphogenesis apoptotic process cell death programmed cell death defense response protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process response to temperature stimulus pigment metabolic process flavonoid metabolic process anthocyanin-containing compound metabolic process tissue development regulation of meristem growth meristem development meristem maintenance meristem growth regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to biotic stimulus defense response to bacterium positive regulation of defense response to bacterium positive regulation of response to external stimulus regulation of response to stress response to bacterium response to external biotic stimulus regulation of defense response to bacterium response to other organism response to external stimulus defense response to other organism positive regulation of defense response response to red light photoprotection plant-type cell wall organization or biogenesis regulation of cell wall organization or biogenesis cell wall organization or biogenesis regulation of cellular component biogenesis cellular component biogenesis plant-type cell wall biogenesis cell wall biogenesis plant-type secondary cell wall biogenesis regulation of secondary cell wall biogenesis rhythmic process inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process circadian rhythm calcium ion homeostasis regulation of cytosolic calcium ion concentration cellular homeostasis chemical homeostasis circadian regulation of calcium ion oscillation intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis response to light intensity response to absence of light leaf morphogenesis shoot system morphogenesis plant organ morphogenesis regulation of shoot system morphogenesis regulation of leaf morphogenesis leaf development shoot system development regulation of plant organ morphogenesis phyllome development response to magnetism detection of light stimulus detection of external stimulus detection of stimulus detection of abiotic stimulus regulation of circadian rhythm response to high light intensity regulation of hydrogen peroxide metabolic process reactive oxygen species metabolic process hydrogen peroxide metabolic process regulation of reactive oxygen species metabolic process stomatal movement response to low light intensity stimulus response to low fluence blue light stimulus by blue low-fluence system phototropism tropism response to lipid response to strigolactone response to organic cyclic compound regulation of systemic acquired resistance systemic acquired resistance defense response to symbiont positive regulation of systemic acquired resistance response to far red light programmed cell death in response to reactive oxygen species cellular response to oxidative stress cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to singlet oxygen response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus response to singlet oxygen cellular response to stress singlet oxygen-mediated programmed cell death nucleoside phosphate metabolic process flavin-containing compound metabolic process flavin adenine dinucleotide metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process localization transport regulation of hormone levels auxin transport hormone transport regulation of biological quality establishment of localization regulation of localization monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity positive regulation of molecular function regulation of monoatomic anion transport positive regulation of monoatomic ion transport monoatomic anion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport positive regulation of cellular process regulation of monoatomic ion transmembrane transporter activity regulation of transport positive regulation of anion channel activity regulation of monoatomic ion transport regulation of monoatomic anion transmembrane transport regulation of anion channel activity positive regulation of anion transmembrane transport positive regulation of monoatomic anion transport transmembrane transport regulation of molecular function regulation of transmembrane transport positive regulation of transport positive regulation of transporter activity monoatomic anion transport positive regulation of ion transmembrane transporter activity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018394	Cryptochrome/DNA photolyase class 1, conserved site, C-terminal	Conserved Site
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A	IPR006050	DNA photolyase, N-terminal	Domain
A	IPR020978	Cryptochrome C-terminal	Domain
A	IPR005101	Cryptochrome/DNA photolyase, FAD-binding domain	Domain
A	IPR014134	Cryptochrome, plant	Family
A	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
A	IPR002081	Cryptochrome/DNA photolyase class 1	Family
A	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily

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.