4U8H

Crystal Structure of Mammalian Period-Cryptochrome Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4u8ha2	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d4u8ha1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth C]	d4u8hc2	All alpha proteins	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	Cryptochrome/photolyase FAD-binding domain	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth C]	d4u8hc1	Alpha and beta proteins (a/b)	Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase, N-terminal domain	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

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	e4u8hA1	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	e4u8hA2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
B [auth C]	FAD_binding_7	e4u8hC1	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)
B [auth C]	DNA_photolyase	e4u8hC2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: DNA_photolyase	ECOD (1.6)
C [auth B]	Period_C	e4u8hB1	A: extended segments	X: CRY-binding domain of PER (From Topology)	H: CRY-binding domain of PER (From Topology)	T: CRY-binding domain of PER	F: Period_C	ECOD (1.6)
D	Period_C	e4u8hD1	A: extended segments	X: CRY-binding domain of PER (From Topology)	H: CRY-binding domain of PER (From Topology)	T: CRY-binding domain of PER	F: Period_C	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)
B [auth C]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
B [auth C]	1.25.40.80	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B [auth C]	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, B [auth C]	PF00875	DNA photolyase (DNA_photolyase)	DNA photolyase	This domain binds a light harvesting cofactor.	Domain
A, B [auth C]	PF03441	FAD binding domain of DNA photolyase (FAD_binding_7)	FAD binding domain of DNA photolyase	-	Domain
C [auth B], D	PF12114	Period protein 2/3C-terminal region (Period_C)	Period protein 2/3C-terminal region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	Cryptochrome-2	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding damaged DNA binding protein binding kinase binding enzyme binding protein kinase binding phosphatase binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding molecular transducer activity photoreceptor activity signaling receptor activity single-stranded DNA binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process multicellular organismal process regulation of localization system process regulation of system process negative regulation of transport negative regulation of lipid localization cell communication regulation of glucocorticoid secretion localization regulation of steroid hormone secretion negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality negative regulation of steroid hormone secretion regulation of hormone levels organic substance transport lipid transport regulation of corticosteroid hormone secretion establishment of localization regulation of secretion endocrine hormone secretion lipid export from cell negative regulation of corticosteroid hormone secretion glucocorticoid secretion negative regulation of multicellular organismal process regulation of endocrine process corticosteroid hormone secretion regulation of hormone secretion transport signaling negative regulation of signaling steroid hormone secretion regulation of lipid transport hormone secretion negative regulation of cell communication secretion by cell regulation of secretion by cell signal release regulation of multicellular organismal process negative regulation of glucocorticoid secretion regulation of signaling negative regulation of lipid transport secretion regulation of transport lipid localization export from cell cell-cell signaling endocrine process regulation of lipid localization macromolecule localization hormone transport regulation of cell communication rhythmic process circadian rhythm regulation of circadian rhythm response to stimulus response to activity response to light stimulus response to radiation response to abiotic stimulus sodium-dependent phosphate transport regulation of phosphate transport regulation of sodium-dependent phosphate transport phosphate ion transport inorganic anion transport protein localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport nuclear transport intracellular transport protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization protein localization to organelle establishment of localization in cell protein import into nucleus intracellular protein transport negative regulation of circadian rhythm circadian regulation of gene expression entrainment of circadian clock response to external stimulus photoperiodism entrainment of circadian clock by photoperiod response to organic substance response to hormone response to chemical response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound cellular response to stimulus intracellular receptor signaling pathway response to lipid regulation of signal transduction hormone-mediated signaling pathway cellular response to endogenous stimulus negative regulation of intracellular steroid hormone receptor signaling pathway response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway signal transduction cellular response to organic substance cellular response to steroid hormone stimulus response to organic cyclic compound cellular response to hormone stimulus negative regulation of response to stimulus intracellular corticosteroid receptor signaling pathway cellular response to organic cyclic compound negative regulation of signal transduction negative regulation of glucocorticoid receptor signaling pathway intracellular glucocorticoid receptor signaling pathway regulation of glucocorticoid receptor signaling pathway cellular response to chemical stimulus steroid hormone mediated signaling pathway regulation of response to stimulus cellular response to lipid nuclear receptor signaling pathway intracellular steroid hormone receptor signaling pathway lipid storage maintenance of location transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen cytosol extracellular region
C [auth B], D	Period circadian protein homolog 2	pre-mRNA binding RNA binding binding organic cyclic compound binding nucleic acid binding transcription factor binding transcription coregulator binding transcription corepressor binding protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding pre-mRNA binding RNA binding binding organic cyclic compound binding nucleic acid binding transcription factor binding transcription coregulator binding transcription corepressor binding protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding histone deacetylase binding enzyme binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase binding kinase binding DNA-binding transcription factor binding histone methyltransferase binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding identical protein binding	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process cellular developmental process cell development regulation of neurogenesis regulation of cell differentiation nervous system development regulation of cell development regulation of nervous system development multicellular organism development neurogenesis cell differentiation anatomical structure development regulation of multicellular organismal process system development rhythmic process circadian rhythm regulation of circadian rhythm negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process organonitrogen compound metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal response to stimulus response to stress response to ischemia lactate biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process organic hydroxy compound metabolic process carboxylic acid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process lactate metabolic process organic hydroxy compound biosynthetic process small molecule metabolic process monocarboxylic acid metabolic process regulation of tube diameter system process regulation of tube size regulation of system process circulatory system process regulation of blood circulation regulation of vasoconstriction vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality blood circulation vasoconstriction regulation of anatomical structure size negative regulation of circadian rhythm circadian regulation of gene expression fatty acid metabolic process cellular lipid metabolic process lipid metabolic process negative regulation of cell population proliferation cell population proliferation fat cell proliferation regulation of cell population proliferation regulation of fat cell proliferation negative regulation of fat cell proliferation homeostatic process positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process protein localization regulation of localization establishment of protein localization nitrogen compound transport cell communication localization cellular macromolecule localization regulation of peptide hormone secretion regulation of hormone levels organic substance transport establishment of protein localization to extracellular region protein secretion establishment of localization regulation of protein secretion regulation of secretion cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport signaling hormone secretion protein localization to extracellular region peptide secretion secretion by cell regulation of secretion by cell amide transport signal release regulation of signaling secretion regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling export from cell regulation of protein transport peptide transport protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion response to light stimulus entrainment of circadian clock response to external stimulus photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod monosaccharide metabolic process carbohydrate metabolic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process gluconeogenesis hexose biosynthetic process glucose metabolic process regulation of molecular function regulation of DNA binding regulation of binding negative regulation of binding negative regulation of transcription regulatory region DNA binding negative regulation of molecular function regulation of transcription regulatory region DNA binding negative regulation of DNA binding circadian regulation of translation organonitrogen compound biosynthetic process post-transcriptional regulation of gene expression translation regulation of translation negative regulation of termination of DNA-templated transcription protein-containing complex disassembly regulation of protein-containing complex disassembly cellular component disassembly negative regulation of cellular component organization regulation of termination of DNA-templated transcription regulation of cellular component organization DNA-templated transcription termination cellular component organization negative regulation of protein-containing complex disassembly cellular component organization or biogenesis protein-containing complex organization cell cycle regulation of cell cycle transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II carboxylic acid transmembrane transport establishment of localization in cell regulation of amino acid transport organic acid transmembrane transport carboxylic acid transport import across plasma membrane neurotransmitter transport organic acid transport transmembrane transport acidic amino acid transport regulation of amino acid import across plasma membrane regulation of transmembrane transport dicarboxylic acid transport L-alpha-amino acid transmembrane transport amino acid import across plasma membrane neurotransmitter uptake L-glutamate transmembrane transport import into cell amino acid transmembrane transport amino acid neurotransmitter reuptake L-amino acid transport L-glutamate import regulation of L-glutamate import across plasma membrane regulation of amino acid transmembrane transport neurotransmitter reuptake regulation of glutamate uptake involved in transmission of nerve impulse regulation of neurotransmitter uptake L-glutamate import across plasma membrane organic anion transport glutamate reuptake regulation of neurotransmitter transport amino acid transport amine transport regulation of organic acid transport regulation of amine transport regulation of amino acid uptake involved in synaptic transmission glucan biosynthetic process polysaccharide biosynthetic process energy derivation by oxidation of organic compounds glycogen metabolic process generation of precursor metabolites and energy glycogen biosynthetic process polysaccharide metabolic process glucan metabolic process energy reserve metabolic process protein-DNA complex organization chromatin organization chromatin remodeling fat cell differentiation white fat cell differentiation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
A, B [auth C]	IPR036155	Cryptochrome/photolyase, N-terminal domain superfamily	Homologous Superfamily
A, B [auth C]	IPR002081	Cryptochrome/DNA photolyase class 1	Family
A, B [auth C]	IPR036134	Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily	Homologous Superfamily
A, B [auth C]	IPR006050	DNA photolyase, N-terminal	Domain
A, B [auth C]	IPR005101	Cryptochrome/DNA photolyase, FAD-binding domain	Domain
C [auth B], D	IPR013655	PAS fold-3	Domain
C [auth B], D	IPR022728	Period circadian-like, C-terminal	Domain
C [auth B], D	IPR000014	PAS domain	Domain
C [auth B], D	IPR048814	Period circadian protein homolog 1-3, PAS-A domain	Domain
C [auth B], D	IPR035965	PAS domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.