8DD7

The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless

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	PF03441	e8dd7A1	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: PF03441	ECOD (1.6)
A	PF00875	e8dd7A2	A: a/b three-layered sandwiches	X: HUP domain-like	H: HUP domains (From Topology)	T: HUP domains	F: PF00875	ECOD (1.6)

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
B	PF05029	Timeless PAB domain (TIMELESS_C)	Timeless PAB domain	The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, b ...	The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2) [1]. mTim has been shown to be essential for embryonic development, but does not have substantiated circadian function[2]. This entry corresponds to the PAB (PARP-1-binding domain) [3].	Domain
B	PF04821	Timeless protein (TIMELESS)	Timeless protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Methylated-DNA--protein-cysteine methyltransferase,Cryptochrome-1 fusion	DNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity methylated-DNA-[protein]-cysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding DNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity methylated-DNA-[protein]-cysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding metal ion binding small molecule binding FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding anion binding nucleotide binding heterocyclic compound binding blue light photoreceptor activity molecular transducer activity photoreceptor activity signaling receptor activity	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair DNA modification macromolecule modification methylation 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 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 regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic 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 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 regulation of cellular biosynthetic process negative regulation of biosynthetic process response to light stimulus response to radiation response to abiotic stimulus response to blue light multicellular organismal process system process sensory perception nervous system process magnetoreception rhythmic process circadian rhythm intracellular receptor signaling pathway signaling cellular response to radiation cellular response to environmental stimulus cell communication cellular response to light stimulus cellular response to abiotic stimulus signal transduction blue light signaling pathway cellular response to blue light response to magnetism entrainment of circadian clock response to external stimulus regulation of circadian rhythm circadian sleep/wake cycle, sleep circadian sleep/wake cycle rhythmic behavior regulation of circadian sleep/wake cycle regulation of behavior behavior circadian behavior regulation of multicellular organismal process sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle process circadian regulation of gene expression detection of light stimulus detection of external stimulus detection of light stimulus involved in magnetoreception sensory perception of light stimulus detection of abiotic stimulus detection of stimulus detection of light stimulus involved in sensory perception detection of stimulus involved in sensory perception photoperiodism entrainment of circadian clock by photoperiod phototransduction UV-A, blue light phototransduction locomotory behavior locomotor rhythm gravitaxis taxis response to gravity locomotion	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity cytoplasm cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen perinuclear region of cytoplasm
B	Protein timeless,Methylated-DNA--protein-cysteine methyltransferase fusion	DNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity methylated-DNA-[protein]-cysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding DNA binding binding organic cyclic compound binding nucleic acid binding catalytic activity, acting on a protein transferase activity, transferring one-carbon groups S-methyltransferase activity protein methyltransferase activity methylated-DNA-[protein]-cysteine S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport regulation of protein localization transport nuclear transport regulation of protein localization to nucleus localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport regulation of protein localization transport nuclear transport regulation of protein localization to nucleus localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization establishment of localization in cell protein import into nucleus regulation of intracellular transport regulation of biological process regulation of transport organic substance transport biological regulation regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization establishment of protein localization to organelle protein transport regulation of cellular localization macromolecule localization protein localization to organelle regulation of intracellular protein transport cellular process intracellular protein transport cellular response to stimulus response to light stimulus response to stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus rhythmic process entrainment of circadian clock circadian rhythm response to external stimulus regulation of circadian rhythm behavior multicellular organismal process reproductive process multicellular organismal reproductive process reproductive behavior mating behavior copulation circadian sleep/wake cycle, sleep circadian sleep/wake cycle rhythmic behavior regulation of circadian sleep/wake cycle regulation of behavior circadian behavior regulation of multicellular organismal process sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle process photoperiodism import into cell positive regulation of cellular component organization regulation of cellular component organization positive regulation of biological process vesicle-mediated transport cellular component organization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport endocytosis primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stress DNA damage response response to stress metabolic process macromolecule metabolic process DNA repair energy taxis negative phototaxis negative energy taxis taxis phototaxis locomotion regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cell communication negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling locomotory behavior locomotor rhythm heart process system process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation regulation of biological quality heart contraction circadian regulation of heart rate blood circulation regulation of heart rate multicellular organismal-level homeostasis homeostatic process temperature homeostasis circadian temperature homeostasis DNA-templated DNA replication maintenance of fidelity regulation of primary metabolic process negative regulation of DNA-templated DNA replication negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process DNA-templated DNA replication negative regulation of DNA replication negative regulation of metabolic process regulation of macromolecule metabolic process DNA replication regulation of DNA-templated DNA replication replication fork arrest negative regulation of DNA metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication developmental process eclosion eclosion rhythm multicellular organism development anatomical structure development organism emergence from protective structure DNA modification macromolecule modification methylation	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle replication fork protection complex protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle replication fork protection complex protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear replication fork nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle replication fork non-membrane-bounded organelle nuclear lumen nucleoplasm perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008332	Methylguanine DNA methyltransferase, ribonuclease-like domain	Domain
A	IPR036217	Methylated DNA-protein cysteine methyltransferase, DNA binding domain	Homologous Superfamily
A	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A	IPR036631	Methylated DNA-protein cysteine methyltransferase domain superfamily	Homologous Superfamily
A	IPR014048	Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding	Domain
A	IPR001497	Methylated-DNA-[protein]-cysteine S-methyltransferase, active site	Active Site
A	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
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
A	IPR006050	DNA photolyase, N-terminal	Domain
A	IPR005101	Cryptochrome/DNA photolyase, FAD-binding domain	Domain
B	IPR007725	Timeless, C-terminal	Domain
B	IPR044998	Timeless	Family
B	IPR006906	Timeless, N-terminal	Domain
B	IPR008332	Methylguanine DNA methyltransferase, ribonuclease-like domain	Domain
B	IPR036217	Methylated DNA-protein cysteine methyltransferase, DNA binding domain	Homologous Superfamily
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR036631	Methylated DNA-protein cysteine methyltransferase domain superfamily	Homologous Superfamily
B	IPR014048	Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding	Domain
B	IPR001497	Methylated-DNA-[protein]-cysteine S-methyltransferase, active site	Active Site

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 R01GM133198.

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8DD7

The Cryo-EM structure of Drosophila Cryptochrome in complex with Timeless

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage